Ubiquitin in regulation of spindle apparatus and its positioning: implications in development and disease

Emerging data implicates ubiquitination, a post-translational modification, in regulating essential cellular events, one of them being mitosis. In this review we discuss how various E3 ligases modulate the cortical proteins such as dynein, LGN, NuMa, Gα, along with polymerization, stability, and integrity of spindles. These are responsible for regulating symmetric cell division. Some of the ubiquitin ligases regulating these proteins include PARK2, BRCA1/BARD1, MGRN1, SMURF2, and SIAH1; these play a pivotal role in the correct positioning of the spindle apparatus. A direct connection between developmental or various pathological disorders and the ubiquitination mediated cortical regulation is rather speculative, though deletions or mutations in them lead to developmental disorders and disease conditions.

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Chain reactions: molecular mechanisms of RBR ubiquitin ligases

Biochemical Society Transactions ◽

10.1042/bst20200237 ◽

2020 ◽

Vol 48 (4) ◽

pp. 1737-1750 ◽

Cited By ~ 2

Author(s):

Thomas R. Cotton ◽

Bernhard C. Lechtenberg

Keyword(s):

Molecular Mechanisms ◽

Catalytic Mechanism ◽

Ubiquitin Ligases ◽

Post Translational Modification ◽

E3 Ligases ◽

Chain Reactions ◽

The Family ◽

Domain Organisation ◽

Almost All ◽

Unique Domain

Ubiquitination is a fundamental post-translational modification that regulates almost all aspects of cellular signalling and is ultimately catalysed by the action of E3 ubiquitin ligases. The RING-between-RING (RBR) family of E3 ligases encompasses 14 distinct human enzymes that are defined by a unique domain organisation and catalytic mechanism. Detailed characterisation of several RBR ligase family members in the last decade has revealed common structural and mechanistic features. At the same time these studies have highlighted critical differences with respect to autoinhibition, activation and catalysis. Importantly, the majority of RBR E3 ligases remain poorly studied, and thus the extent of diversity within the family remains unknown. In this mini-review we outline the current understanding of the RBR E3 mechanism, structure and regulation with a particular focus on recent findings and developments that will shape the field in coming years.

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Ubiquitination, Biotech Startups, and the Future of TRIM Family Proteins: A TRIM-Endous Opportunity

Cells ◽

10.3390/cells10051015 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1015

Author(s):

Utsa Bhaduri ◽

Giuseppe Merla

Keyword(s):

Drug Discovery ◽

Protein Degradation ◽

Ubiquitin Ligase ◽

Genetic Disorders ◽

E3 Ubiquitin Ligase ◽

Ubiquitin Ligases ◽

E3 Ubiquitin Ligases ◽

Post Translational Modification ◽

Disease Biology ◽

The Future

Ubiquitination is a post-translational modification that has pivotal roles in protein degradation and diversified cellular processes, and for more than two decades it has been a subject of interest in the biotech or biopharmaceutical industry. Tripartite motif (TRIM) family proteins are known to have proven E3 ubiquitin ligase activities and are involved in a multitude of cellular and physiological events and pathophysiological conditions ranging from cancers to rare genetic disorders. Although in recent years many kinds of E3 ubiquitin ligases have emerged as the preferred choices of big pharma and biotech startups in the context of protein degradation and disease biology, from a surface overview it appears that TRIM E3 ubiquitin ligases are not very well recognized yet in the realm of drug discovery. This article will review some of the blockbuster scientific discoveries and technological innovations from the world of ubiquitination and E3 ubiquitin ligases that have impacted the biopharma community, from biotech colossuses to startups, and will attempt to evaluate the future of TRIM family proteins in the province of E3 ubiquitin ligase-based drug discovery.

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The Multifaceted Roles of USP15 in Signal Transduction

International Journal of Molecular Sciences ◽

10.3390/ijms22094728 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4728

Author(s):

Tanuza Das ◽

Eun Joo Song ◽

Eunice EunKyeong Kim

Keyword(s):

Signal Transduction ◽

Signaling Pathways ◽

Cellular Networks ◽

Clinical Applications ◽

Regulatory Mechanisms ◽

Signaling Networks ◽

Post Translational Modification ◽

Comprehensive Overview ◽

E3 Ligases ◽

Disease Markers

Ubiquitination and deubiquitination are protein post-translational modification processes that have been recognized as crucial mediators of many complex cellular networks, including maintaining ubiquitin homeostasis, controlling protein stability, and regulating several signaling pathways. Therefore, some of the enzymes involved in ubiquitination and deubiquitination, particularly E3 ligases and deubiquitinases, have attracted attention for drug discovery. Here, we review recent findings on USP15, one of the deubiquitinases, which regulates diverse signaling pathways by deubiquitinating vital target proteins. Even though several basic previous studies have uncovered the versatile roles of USP15 in different signaling networks, those have not yet been systematically and specifically reviewed, which can provide important information about possible disease markers and clinical applications. This review will provide a comprehensive overview of our current understanding of the regulatory mechanisms of USP15 on different signaling pathways for which dynamic reverse ubiquitination is a key regulator.

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Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy

International Journal of Molecular Sciences ◽

10.3390/ijms22020791 ◽

2021 ◽

Vol 22 (2) ◽

pp. 791

Author(s):

Qi Liu ◽

Bayonle Aminu ◽

Olivia Roscow ◽

Wei Zhang

Keyword(s):

Tumor Microenvironment ◽

Cancer Therapy ◽

Therapeutic Agents ◽

Biological Processes ◽

Post Translational Modification ◽

E3 Ligases ◽

Tumor Microenvironments ◽

Cellular Immune ◽

Ubiquitin Conjugating Enzymes ◽

Cellular Components

Tumor microenvironments are composed of a myriad of elements, both cellular (immune cells, cancer-associated fibroblasts, mesenchymal stem cells, etc.) and non-cellular (extracellular matrix, cytokines, growth factors, etc.), which collectively provide a permissive environment enabling tumor progression. In this review, we focused on the regulation of tumor microenvironment through ubiquitination. Ubiquitination is a reversible protein post-translational modification that regulates various key biological processes, whereby ubiquitin is attached to substrates through a catalytic cascade coordinated by multiple enzymes, including E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes and E3 ubiquitin ligases. In contrast, ubiquitin can be removed by deubiquitinases in the process of deubiquitination. Here, we discuss the roles of E3 ligases and deubiquitinases as modulators of both cellular and non-cellular components in tumor microenvironment, providing potential therapeutic targets for cancer therapy. Finally, we introduced several emerging technologies that can be utilized to develop effective therapeutic agents for targeting tumor microenvironment.

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Highly Specialized Ubiquitin-Like Modifications: Shedding Light into the UFM1 Enigma

Biomolecules ◽

10.3390/biom11020255 ◽

2021 ◽

Vol 11 (2) ◽

pp. 255

Author(s):

Katharina F. Witting ◽

Monique P.C. Mulder

Keyword(s):

Dna Repair ◽

Stress Response ◽

Embryonic Development ◽

Er Stress ◽

Unmet Needs ◽

Biological Function ◽

Post Translational Modification ◽

Er Stress Response ◽

Cellular Events ◽

Complex Signaling

Post-translational modification with Ubiquitin-like proteins represents a complex signaling language regulating virtually every cellular process. Among these post-translational modifiers is Ubiquitin-fold modifier (UFM1), which is covalently attached to its substrates through the orchestrated action of a dedicated enzymatic cascade. Originally identified to be involved embryonic development, its biological function remains enigmatic. Recent research reveals that UFM1 regulates a variety of cellular events ranging from DNA repair to autophagy and ER stress response implicating its involvement in a variety of diseases. Given the contribution of UFM1 to numerous pathologies, the enzymes of the UFM1 cascade represent attractive targets for pharmacological inhibition. Here we discuss the current understanding of this cryptic post-translational modification especially its contribution to disease as well as expand on the unmet needs of developing chemical and biochemical tools to dissect its role.

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Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation

Physiological Genomics ◽

10.1152/physiolgenomics.00031.2016 ◽

2016 ◽

Vol 48 (7) ◽

pp. 502-512 ◽

Cited By ~ 31

Author(s):

Barbara Medvar ◽

Viswanathan Raghuram ◽

Trairak Pisitkun ◽

Abhijit Sarkar ◽

Mark A. Knepper

Keyword(s):

Human Genome ◽

Large Scale ◽

E3 Ligase ◽

Ubiquitin Ligases ◽

Bayes Rule ◽

E3 Ubiquitin Ligases ◽

E3 Ligases ◽

Aquaporin 2 ◽

Large Scale Data ◽

Level Data

Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, “What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?” using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database ( https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/ ). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover.

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Comprehensive Analysis of E3 Ubiquitin Ligases Reveals Ring Finger Protein 223 as a Novel Oncogene Activated by KLF4 in Pancreatic Cancer

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.738709 ◽

2021 ◽

Vol 9 ◽

Author(s):

Lei Feng ◽

Jieqing Wang ◽

Jianmin Zhang ◽

Jingfang Diao ◽

Longguang He ◽

...

Keyword(s):

Pancreatic Cancer ◽

Transcriptional Activation ◽

Prognostic Significance ◽

Ring Finger ◽

Ubiquitin Ligases ◽

The Cancer Genome Atlas ◽

Differentially Expressed ◽

E3 Ubiquitin Ligases ◽

E3 Ligases ◽

Elevated Expression

Pancreatic cancer is one of the major malignancies and causes of mortality worldwide. E3 ubiquitin–protein ligases transfer activated ubiquitin from ubiquitin-conjugating enzymes to protein substrates and confer substrate specificity in cancer. In this study, we first downloaded data from The Cancer Genome Atlas pancreatic adenocarcinoma dataset, acquired all 27 differentially expressed genes (DEGs), and identified genomic alterations. Then, the prognostic significance of DEGs was analyzed, and eight DEGs (MECOM, CBLC, MARCHF4, RNF166, TRIM46, LONRF3, RNF39, and RNF223) and two clinical parameters (pathological N stage and T stage) exhibited prognostic significance. RNF223 showed independent significance as an unfavorable prognostic marker and was chosen for subsequent analysis. Next, the function of RNF223 in the pancreatic cancer cell lines ASPC-1 and PANC-1 was investigated, and RNF223 silencing promoted pancreatic cancer growth and migration. To explore the potential targets and pathways of RNF223 in pancreatic cancer, quantitative proteomics was applied to analyze differentially expressed proteins, and metabolism-related pathways were primarily enriched. Finally, the reason for the elevated expression of RNF223 was analyzed, and KLF4 was shown to contribute to the increased expression of RNF233. In conclusion, this study comprehensively analyzed the clinical significance of E3 ligases. Functional assays revealed that RNF223 promotes cancer by regulating cell metabolism. Finally, the elevated expression of RNF223 was attributed to KLF4-mediated transcriptional activation. This study broadens our knowledge regarding E3 ubiquitin ligases and signal transduction and provides novel markers and therapeutic targets in pancreatic cancer.

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Regulation of cell cycle drivers by Cullin-RING ubiquitin ligases

Experimental & Molecular Medicine ◽

10.1038/s12276-020-00508-4 ◽

2020 ◽

Vol 52 (10) ◽

pp. 1637-1651 ◽

Cited By ~ 1

Author(s):

Sang-Min Jang ◽

Christophe E. Redon ◽

Bhushan L. Thakur ◽

Meriam K. Bahta ◽

Mirit I. Aladjem

Keyword(s):

Cell Cycle ◽

Cell Division ◽

Cell Cycle Progression ◽

Ubiquitin Ligases ◽

Anaphase Promoting Complex ◽

Cycle Progression ◽

Cellular Processes ◽

Cellular Pathways ◽

Regulation Of Cell Cycle ◽

F Box Protein

Abstract The last decade has revealed new roles for Cullin-RING ubiquitin ligases (CRLs) in a myriad of cellular processes, including cell cycle progression. In addition to CRL1, also named SCF (SKP1-Cullin 1-F box protein), which has been known for decades as an important factor in the regulation of the cell cycle, it is now evident that all eight CRL family members are involved in the intricate cellular pathways driving cell cycle progression. In this review, we summarize the structure of CRLs and their functions in driving the cell cycle. We focus on how CRLs target key proteins for degradation or otherwise alter their functions to control the progression over the various cell cycle phases leading to cell division. We also summarize how CRLs and the anaphase-promoting complex/cyclosome (APC/C) ligase complex closely cooperate to govern efficient cell cycle progression.

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Regulation of the meiotic divisions of mammalian oocytes and eggs

Biochemical Society Transactions ◽

10.1042/bst20170493 ◽

2018 ◽

Vol 46 (4) ◽

pp. 797-806 ◽

Cited By ~ 10

Author(s):

Jessica R. Sanders ◽

Keith T. Jones

Keyword(s):

Cell Division ◽

Luteinizing Hormone ◽

Spindle Assembly Checkpoint ◽

Asymmetric Cell Division ◽

Homologous Chromosomes ◽

Mammalian Oocyte ◽

Cellular Events ◽

The Hours ◽

Meiosis I

Initiated by luteinizing hormone and finalized by the fertilizing sperm, the mammalian oocyte completes its two meiotic divisions. The first division occurs in the mature Graafian follicle during the hours preceding ovulation and culminates in an extreme asymmetric cell division and the segregation of the two pairs of homologous chromosomes. The newly created mature egg rearrests at metaphase of the second meiotic division prior to ovulation and only completes meiosis following a Ca2+ signal initiated by the sperm at gamete fusion. Here, we review the cellular events that govern the passage of the oocyte through meiosis I with a focus on the role of the spindle assembly checkpoint in regulating its timing. In meiosis II, we examine how the egg achieves its arrest and how the fertilization Ca2+ signal allows the initiation of embryo development.

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