Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: UNIPROT:P62988 (Ubiquitin)
 4,326 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A 30-kDa enzyme from red blood cells responsible for the recycling of free Ubiquitin has been characterized. This enzyme was previously known to have a Ubiquitin-C-terminal hydrolase activity on adducts of Ubiquitin to small compounds. In this study it was shown that the 30-kDa enzyme contained Ubiquitin-C-terminal hydrolase activity toward biosynthetic precursors of Ub as well as isopeptidase activity toward Ubiquitin histone conjugates. Detailed inhibition experiments with Ubiquitin aldehyde, iodoacetamide, and heat inactivation showed that the enzyme isopeptidase activity was affected differently from its hydrolase activity.
 ...
PMID:Characterization of the 30-kDa enzyme from red blood cells that cleaves ubiquitin-protein conjugates. 799 48

Polyubiquitination is a death signal for proteins and condemns proteins to subsequent degradation by the 26S proteasome. However, recent studies imply that monoubiquitination and polyubiquitination of proteins do not necessarily result in protein degradation but play an important role in the execution of various biological events such as signal transduction and transcription. Ubiquitin was originally identified as a moiety attached to histones, and this as well as other histone modifications may play an important role for transcription and various other DNA-dependent processes. Considerable progress has been made in linking several histone modifications with chromatin dynamics in transcription. Acetylation of histones has been intimately linked to activation of transcription, while deacetylation is concomitant with repression of transcription. Although other histone modifications such as methylation, phosphorylation, and ubiquitination have been correlated with transcriptionally competent or inactive chromatin, the enzymes that mediate these modifications are only now being discovered. The identification of these histone-modifying enzymes may provide valuable insights into the role and function of histone modifications such as ubiquitination in transcription as well as other DNA-dependent processes. Recently, we have used various in vitro assays to show that the coactivator TAF(II)250 possesses both ubiquitin-activating and ubiquitin-conjugating activities, which monoubiquitinate histone H1. Here, we describe the methods used to identify this bifunctional enzyme: (1) in-gel activity assay; (2) protein-transfer membrane activity assay; and (3) in-solution activity assay. These methods have been successfully used to identify various histone-modifying enzymes and protein kinases. In this article we contribute a short review of the history of the methods used to study ubiquitination of proteins and histone modification. We provide protocols for in-gel, protein-transfer membrane, and in-solution ubiquitination assays. A discussion of the general use of the provided protocols, their limitations, and future perspectives are presented. The described methods provide useful tools for the identification of not only novel histone-modifying enzymes but also other protein-modifying enzymes that act in a variety of biological events.
 ...
PMID:In vitro assays to study protein ubiquitination in transcription. 1205 79

Loss of the tumour suppressor BRCA1 results in profound chromosomal instability. The fundamental defect underlying this catastrophic phenotype is not yet known. In vivo, BRCA1 forms a heterodimeric complex with BARD1. Both proteins contain an N-terminal zinc RING-finger domain which confers E3 ubiquitin ligase activity. We have isolated full-length human BRCA1/BARD1 complex and have shown that it has a dual E3 ubiquitin ligase activity. First, it mediates the monoubiquitylation of nucleosome core histones in vitro, including the variant histone H2AX that co-localizes with BRCA1 at sites of DNA damage. Secondly, BRCA1/BARD1 catalyses the formation of multiple polyubiquitin chains on itself. Remarkably, this auto-polyubiquitylation potentiates the E3 ubiquitin ligase activity of the BRCA1/BARD1 complex >20-fold. Even though BRCA1 has been reported to associate with a C-terminal ubiquitin hydrolase, BAP1, this enzyme does not appear to function in the deubiquitylation of the BRCA1/BARD1 complex.
 ...
PMID:Activation of the E3 ligase function of the BRCA1/BARD1 complex by polyubiquitin chains. 1248 96

Eukaryotic transcription is one of the most complex cellular processes and constitutes the first step in protein synthesis. Ubiquitination and subsequent degradation by the 26 S proteasome, on the other hand, represents the final chapter in the life of a protein. Intriguingly, ubiquitin and the ubiquitin- proteasome system play vital roles in the regulation of transcription. Ubiquitin has dual modus operandi: firstly, ubiquitin functions via the 26 S proteasome--it is tagged to components of the transcription machinery, marking them for degradation via the proteasome, which results in the proper exchange of complexes during transcription and the prompt removal of activators after each round of transcription; and secondly, ubiquitin can function independently of the proteasome--histone ubiquitination results in heterochromatin relaxation and assembly of transcription complexes on the promoter, and ubiquitination of transcription factors enhances their transcriptional-activation function. Although ubiquitin and the ubiquitin-proteasome system were initially perceived as a graveyard for proteins, recent advances in molecular biological techniques have redefined their role as a regulatory system that influences the fate of many cellular processes, such as apoptosis, transcription and cell cycle progression.
 ...
PMID:Ubiquitin and control of transcription. 1625 Aug 98

Ubiquitin, a key component in an ATP-dependent proteolytic pathway, participates in the response of various eucaryotic organisms to high temperature stress. Our objective was to determine if ubiquitin serves a similar capacity for metabolizing altered proteins in higher plants during stress. Degradation of total proteins was measured, and ubiquitin pools (free versus conjugated) were extracted with an improved protocol from wheat (Triticum aestivum L. cv Len) roots treated at 22, 27, 32, 37, and 42 degrees C for 1 hour and assayed by western blots and radioimmunoassays. Heat-shock protein synthesis was detected by in vivo labeling and autoradiography. Mean half-life of total root proteins decreased from 51 hours at 22 degrees C to 23 hours at 40 degrees C. Ubiquitin pools were extracted better and proteolysis was slowed more by the improved protocol than by a conventional procedure for plant proteins. Amounts of high molecular mass conjugates were elevated and levels of low molecular mass conjugates and free ubiquitin were depressed when roots were treated at 37 or 42 degrees C than at lower temperatures; the same high temperatures also induced synthesis of heat-shock proteins. We concluded that high temperatures increase breakdown of root proteins, which are degraded via the ubiquitin proteolytic pathway. A conjugate with an apparent molecular mass of 23 kilodaltons was tentatively identified as an ubiquitinated histone.
 ...
PMID:Ubiquitin Pool Modulation and Protein Degradation in Wheat Roots during High Temperature Stress. 1666 43

The small (76 amino acids) and highly conserved ubiquitin protein plays key roles in the physiology of eukaryotic cells. Protein ubiquitylation has emerged as one of the most important intracellular signaling mechanisms, and in 2004 the Nobel Prize was awarded to Aaron Ciechanower, Avram Hersko, and Irwin Rose for their pioneering studies of the enzymology of ubiquitin attachment. One of the most common features of protein ubiquitylation is the attachment of polyubiquitin chains (four or more ubiquitin moieties attached to each other), which is a widely used mechanism to target proteins for degradation via the 26S proteosome. However, it is noteworthy that the first ubiquitylated protein to be identified was histone H2A, to which a single ubiquitin moiety is most commonly attached. Following this discovery, other histones (H2B, H3, H1, H2A.Z, macroH2A), as well as many nonhistone proteins, have been found to be monoubiquitylated. The role of monoubiquitylation is still elusive because a single ubiquitin moiety is not sufficient to target proteins for turnover, and has been hypothesized to control the assembly or disassembly of multiprotein complexes by providing a protein-binding site. Indeed, a number of ubiquitin-binding domains have now been identified in both polyubiquitylated and monoubiquitylated proteins. Despite the early discovery of ubiquitylated histones, it has only been in the last five or so years that we have begun to understand how histone ubiquitylation is regulated and what roles it plays in the cell. This review will discuss current research on the factors that regulate the attachment and removal of ubiquitin from histones, describe the relationship of histone ubiquitylation to histone methylation, and focus on the roles of ubiquitylated histones in gene expression.
 ...
PMID:Histone ubiquitylation and the regulation of transcription. 1690 90

Tip60 is a histone acetyl transferase (HAT) and a cofactor of transcription, but also an interaction partner of the Mdm2 oncoprotein. The functional consequences of this interaction are only partially understood and were further explored in this study. We found that Tip60 is capable of selectively inhibiting the Mdm2-mediated conjugation of Nedd8 to p53, whereas it did not affect p53 ubiquitination. In contrast, the known Mdm2 antagonist p14arf preferentially blocked Ubiquitin conjugation by Mdm2. To identify underlying mechanisms, we studied the intracellular localization of Tip60 and Mdm2. Both proteins relocalized each other to the PML nuclear bodies, but a similar localization pattern was observed even in the absence of PML. Analysis of Tip60 deletion mutants revealed that some mutants, while still interacting with Mdm2, failed to relocalize it and to inhibit Mdm2-mediated neddylation, suggesting that these two phenomena require biochemical activities in addition to the mere interaction between the two proteins. For both activities, the HAT domain of Tip60 was not required. We propose that Tip60 can act as a selective antagonist to Mdm2-mediated neddylation but not ubiquitination. Hence, the two different E3 ligase activities of Mdm2 can be regulated individually.
 ...
PMID:Specific inhibition of Mdm2-mediated neddylation by Tip60. 1826 29

The identification of histone methyltransferases and demethylases has uncovered a dynamic methylation system needed to modulate appropriate levels of gene expression. Gene expression levels of various histone demethylases, such as the JARID1 family, show distinct patterns of embryonic and adult expression and respond to different environmental cues, suggesting that histone demethylase protein levels must be tightly regulated for proper development. In our study, we show that the protein level of the yeast histone H3 Lys 4 (H3 K4) demethylase Jhd2/Kdm5 is modulated through polyubiquitination by the E3 ubiquitin ligase Not4 and turnover by the proteasome. We determine that polyubiquitin-mediated degradation of Jhd2 controls in vivo H3 K4 trimethylation and gene expression levels. Finally, we show that human NOT4 can polyubiquitinate human JARID1C/SMCX, a homolog of Jhd2, suggesting that this is likely a conserved mechanism. We propose that Not4 is an E3 ubiquitin ligase that monitors and controls a precise amount of Jhd2 protein so that the proper balance between histone demethylase and histone methyltransferase activities occur in the cell, ensuring appropriate levels of H3 K4 trimethylation and gene expression.
 ...
PMID:Polyubiquitination of the demethylase Jhd2 controls histone methylation and gene expression. 1934 2

Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fully defined. Ubiquitin was proposed to bind proteins to physically bridge H2Bub1 with Set1-COMPASS/Dot1. Alternatively, the bulky ubiquitin was thought to be a "wedge" that loosens the nucleosome for factor access. Contrary to the latter possibility, recent discoveries provide evidence for nucleosome stabilization by H2Bub1 via preventing the constant H2A-H2B eviction. Recent data has also uncovered a "docking-site" on H2B for Set1-COMPASS. Collectively, these findings invoke a model, where ubiquitin acts as a "glue" to bind the nucleosome together for supporting Set1-COMPASS/Dot1 functions. This review provides an overview of these novel findings. Additionally, how H2Bub1 and its deubiquitination might alter the chromatin dynamics during transcription is discussed. Possible models for nucleosome stabilization by ubiquitin are also provided.
 ...
PMID:Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. 2052 15

Over-expressed in numerous cancers, Ubiquitin-like containing PHD Ring Finger 1 (UHRF1, also known as ICBP90 or Np95) is characterized by a SRA domain (Set and Ring Associated) which is found only in the UHRF family. UHRF1 constitutes a complex with histone deacetylase 1 (HDAC1) and DNA methyltransferase 1 (DNMT1) via its SRA domain and represses the expression of several tumour suppressor genes (TSGs) including p16INK4A, hMLH1, BRCA1 and RB1. Conversely, UHRF1 is regulated by other TSGs such as p53 and p73. UHRF1 is hypothetically involved in a macro-molecular protein complex called "ECREM" for "Epigenetic Code Replication Machinery". This complex would be able to duplicate the epigenetic code by acting at the DNA replication fork and by activating the right enzymatic activity at the right moment. There are increasing evidence that UHRF1 is the conductor of this replication process by ensuring the crosstalk between DNA methylation and histone modifications via the SRA and Tandem Tudor Domains, respectively. This cross-talk allows cancer cells to maintain the repression of TSGs during cell proliferation. Several studies showed that down-regulation of UHRF1 expression in cancer cells by natural pharmacological active compounds, favors enhanced expression or re-expression of TSGs, suppresses cell growth and induces apoptosis. This suggests that hindering UHRF1 to exert its role in the duplication of the methylation patterns (DNA + histones) is responsible for inducing apoptosis. In this review, we present UHRF1 expression as a target of several natural products and we discuss their underlying molecular mechanisms and benefits for chemoprevention and chemotherapy.
 ...
PMID:Down-regulation of UHRF1, associated with re-expression of tumor suppressor genes, is a common feature of natural compounds exhibiting anti-cancer properties. 2149 37


<< Previous 1 2 3 4 5 Next >>