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Enzymology and Regulation of SUMO Conjugation and Deconjugation
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Regulation of the tumor suppressor PTEN by SUMO
Paul Fisher. Cell Line Development. Mohamed Al-Rubeai. ABC Transporters - 40 Years on. Anthony M. Molecular Genetics of Dysregulated pH Homeostasis. Jen-Tsan Ashley Chi. Checkpoint Controls and Targets in Cancer Therapy. Members of this family Ubls are post-translational modifiers that are covalently attached to target proteins through lysine residues in the target. Biochemically, the processing and conjugation of these modifiers is remarkably similar, although the individual enzymes and components are usually specific for their individual modifier.
The modification process is dynamic with exact demodification occurring through specific proteases that remove the Ubls and restore the target proteins to their original state. Functionally, Ubl modification can influence many aspects of protein biology including activity, localization, stability, and interactions with partners. Importantly, examples of functional cross-talk between Ub and SUMO modifications have been observed, which provides exciting opportunities for combinatorial regulation of target proteins.
This chapter will introduce basic principles of ubiquitinylation and sumoylation and will also provide a general overview of important terms and concepts that will be explored in more detail in the remaining chapters. Cracking the Ubiquitin Code: the Ubiquitin Toolbox. Ubiquitination, a post-translational modification, regulates a vast array of fundamental biological processes with dysregulation of the dedicated enzymes giving rise to pathologies such as cancer and neurodegenerative diseases.
Assembly and its ensuing removal of this post-translational modification, determining a large variety of biological functions, is executed by a number of enzymes sequentially activating, conjugating, ligating, as well deubiquitinating. Considering the vast impact of ubiquitination on regulating cellular homeostasis, understanding the function of these vast enzyme networks merits the development and innovation of tools.
Thus, advances in synthetic strategies for generating ubiquitin, permitted the development of a plethora of ubiquitin assay reagents and numerous activity-based probes ABPs enable the study of enzymes involved in the complex system of ubiquitination. With ubiquitination playing such a pivotal role in the pathogenesis of a multitude of diseases, the identification of inhibitors for ubiquitin enzymes as well as the development of ABPs and high-throughput assay reagents is of utmost importance. Accordingly, this chapter will review the current state-of-the-art activity-based probes, reporter substrates, and other relevant tools based on Ub as a recognition element while highlighting the need of innovative technologies and unique concepts to study emerging facets of ubiquitin biology.
Open-access article. Further understanding of the cross-talk taking place between protein SUMOylation and ubiquitylation can provide valuable insights into the biological function and turnover of proteins. Recent advances in sample preparation and the development of sensitive mass spectrometers enabled a systems-level view of this cross communication. Here, we highlight the evolution as well as the merits and limitations of the various workflows that have been created to monitor protein SUMOylation and ubiquitylation. Furthermore, this chapter delves into mass spectrometry centered approaches to study the co-occurrence of SUMOylation and ubiquitylation on proteins in a non-biased large-scale fashion using immunoaffinity enrichment that target either the co-modified proteins from cell extracts or the modified peptides of the corresponding proteins.
Lastly, we provide a perspective on methods that will permit the global analysis of endogenous proteins modified by different ubiquitin-like proteins UBLs. In this chapter, we introduce the small ubiquitin-like modifier SUMO and describe how it is attached to target proteins.
What is known about how SUMO attachment changes the function of a target protein is briefly reviewed. The main focus of the chapter is to introduce the various methods for identifying SUMO attachment sites on target proteins using proteomics and mass spectrometry. Finally, we present a future outlook for one newly discovered function of SUMO that will be quite interesting to study using the new proteomics approaches. Since its discovery, the high-affinity interaction between biotin and avidin has formed the basis of numerous tools and techniques in molecular biology and biochemistry.
The post-translational modifications of cellular proteins via conjugation of ubiquitin Ub and ubiquitin-like UbL proteins contribute to crucial cellular processes, such as protein homeostasis and the DNA damage response, yet they are challenging to study due to their dynamic nature, scarcity, and sensitivity to removal by proteases. SUMOylation is an essential post-translational protein modification in various cellular functions. Here, we describe a newly-developed screening system for mammalian SUMOylated proteins in living cells, which is based on split fluorescence protein reconstitution and fluorescence-based cell sorting technique.
We summarized the applicability to other SUMO isoforms and various cell types, which will be able to contribute to broader exploration of the roles of SUMOylation in numerous biological phenomena.
These large-scale protein microarray datasets were integrated to construct a multidimensional SUMO network that can be used to connect substrates to upstream E3 ligases and to predict SUMO-dependent protein-protein interactions. By enhancing our knowledge of the architecture and regulation of the enzyme-substrate network, we can strengthen our understanding of the functional outcomes of SUMO modification in human cells. Ubiquitin is a small protein that can be attached to thousands of substrates via an enzymatic cascade involving an activating enzyme E1 , a conjugating enzyme E2 and a ligase E3.
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Over different human E3 ligases have been found. The identification of specific targets for ubiquitin E3 ligases is challenging. So far, most of the approaches aimed to identify E3-specific substrates rely on indirect evidence. The rationale behind this strategy is that on construction of a linear fusion between an E3 of interest and ubiquitin, this ubiquitin moiety will be employed by the linked E3 to modify its substrates. Subsequently, trapped substrates are purified in denaturing buffers to remove non-covalent interactors.
Starting from the cDNA sequence of an E3 ligase of interest and finishing with the identification of the ubiquitination targets by mass spectrometry-based proteomics, the whole process takes between 4 to 6 weeks. The description of the methodology includes a discussion of potential pitfalls and specific recommendations. The p53 family includes, in addition to the well-known tumour suppressor p53, two additional proteins, p63 and p These proteins are encoded by two different genes, each of them subjected to different activation modes.
All family members have an essential role in either tumourigenesis or morphogenesis. The high degree of identity among the three protein sequences is mirrored by the existence of a common modular protein structure. Despite the homology, p53, p63 or p73 gene inactivation in mice gave rise to different phenotypes indicating that the proteins encoded by these genes play different roles.
While p53 has the central function of tumour suppressor, both p63 and p73 are actively involved in development and differentiation. A complex set of post-translational modifications such as phosphorylation, acetylation, ribosylation, glycosylation, ubiquitylation and SUMOylation, with often-intertwined modes of action regulates p53 family members functions. Ubiquitylation and SUMOylation appear to affect transactivation ability, localization and stabilization of these transcriptional factors and to confer their timely regulated role during differentiation and development.
In this chapter, the role of p53 family members will be described as well as the impact of ubiquitylation and SUMOylation on their functions. Moreover, other ubiquitin-like proteins have also been shown to regulate p53 family members activity. A myriad of processes occurring in each individual cell govern the functions of tissues and the overall activity of multicellular organisms.
Stringent and precise multilevel control of these cellular pathway components dictates the normal functioning of cells. This control, to maintain the homeostasis in the cells, is exercised at various levels including transcription, post-transcription, translation and post-translation. The following sections in this chapter will discuss miRNAs, namely their synthesis and functions, the processes of ubiquitination and sumoylation and how these different level modifications crosstalk with each other in order to regulate the normal and diseased states of individuals.
DNA replication is a tightly regulated conserved process that ensures the faithful transmission of genetic material to define heritable phenotypic traits. Perturbations in this process result in genomic instability, mutagenesis, and diseases, including malignancy. Proteins involved in the initiation, progression, and termination of DNA replication are subject to a plethora of reversible post-translational modifications PTMs to provide a proper temporal and spatial control of replication.
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