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Project description:Transcriptional Regulation by Cullin Ubiquitin Ligases
| PRJNA614537 | ENA
Project description:Cullin-RING E3 ubiquitin ligases (CRL) control a myriad of biological processes by directing numerous protein substrates for proteasomal degradation. Key to CRL activity is the recruitment of the E2 ubiquitin-conjugating enzyme Cdc34 through electrostatic interactions between E3's cullin conserved basic canyon and the acidic C terminus of the E2 enzyme. This report demonstrates that a small-molecule compound, suramin, can inhibit CRL activity by disrupting its ability to recruit Cdc34. Suramin, an antitrypansomal drug that also possesses antitumor activity, was identified here through a fluorescence-based high-throughput screen as an inhibitor of ubiquitination. Suramin was shown to target cullin 1's conserved basic canyon and to block its binding to Cdc34. Suramin inhibits the activity of a variety of CRL complexes containing cullin 2, 3, and 4A. When introduced into cells, suramin induced accumulation of CRL substrates. These observations help develop a strategy of regulating ubiquitination by targeting an E2-E3 interface through small-molecule modulators.
| S-EPMC4833235 | biostudies-literature
Project description:Cullin-RING E3 ubiquitin ligases (CRLs) control a plethora of biological pathways through targeted ubiquitylation of signalling proteins. These modular assemblies use substrate receptor modules to recruit specific targets. Recent efforts have focused on understanding the mechanisms that control the activity state of CRLs through dynamic alterations in CRL architecture. Central to these processes are cycles of cullin neddylation and deneddylation, as well as exchange of substrate receptor modules to re-sculpt the CRL landscape, thereby responding to the cellular requirements to turn over distinct proteins in different contexts. This review is focused on how CRLs are dynamically controlled with an emphasis on how cullin neddylation cycles are integrated with receptor exchange.
| S-EPMC3849489 | biostudies-other
Project description:Ubiquitination is a highly conserved post-translational modification in eukaryotes, well known for targeting proteins for degradation by the 26S proteasome. Proteins destined for proteasomal degradation are selected by E3 ubiquitin ligases. Cullin-RING E3 ubiquitin ligases (CRLs) are the largest superfamily of E3 ubiquitin ligases, with over 400 members known in mammals. These modular complexes are tightly regulated in the cell. In this chapter, we highlight recent structural and biochemical advances shedding light on the assembly and architecture of cullin-RING ligases, their dynamic regulation by a variety of host factors, and their manipulation by viral pathogens and small molecules.
| S-EPMC7205596 | biostudies-literature
Project description:RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s - including the cullin-RING ligase family - are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms - interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners - directing cullin-RING E3-E2 enzyme active sites to modify their specific targets.
| S-EPMC8096640 | biostudies-literature
Project description:BACKGROUND:Cullin-RING E3 ubiquitin ligase complexes play a central role in targeting cellular proteins for ubiquitination-dependent protein turnover through 26S proteasome. Cullin-2 is a member of the Cullin family, and it serves as a scaffold protein for Elongin B and C, Rbx1 and various substrate recognition receptors to form E3 ubiquitin ligases. MAIN BODY OF THE ABSTRACT:First, the composition, structure and the regulation of Cullin-2 based E3 ubiquitin ligases were introduced. Then the targets, the biological functions of complexes that use VHL, Lrr-1, Fem1b, Prame, Zyg-11, BAF250, Rack1 as substrate targeting subunits were described, and their involvement in diseases was discussed. A small molecule inhibitor of Cullins as a potential anti-cancer drug was introduced. Furthermore, proteins with VHL box that might bind to Cullin-2 were described. Finally, how different viral proteins form E3 ubiquitin ligase complexes with Cullin-2 to counter host viral defense were explained. CONCLUSIONS:Cullin-2 based E3 ubiquitin ligases, using many different substrate recognition receptors, recognize a number of substrates and regulate their protein stability. These complexes play critical roles in biological processes and diseases such as cancer, germline differentiation and viral defense. Through the better understanding of their biology, we can devise and develop new therapeutic strategies to treat cancers, inherited diseases and viral infections.
| S-EPMC4878042 | biostudies-literature
Project description:We determined the genomic locations of the Zur binding sites by chromatin immuno-precipitation of cross-linked DNA and hybridization on a tilling oligonucleotide array on exponentially grown cultures of M145 and zur mutant.
2017-05-18 | GSE95760 | GEO
Project description:Cullin-RING ubiquitin ligases (CRL) regulate numerous biological processes in the heart and have been implicated in regulating cardiac hypertrophy. This study aimed to identify novel hypertrophy-modulating CRLs in cardiomyocytes (CM). A functional genomic approach using siRNA-mediated depletion and automated microscopy was employed to screen for cell size-modulating CRLs in neonatal rat CM. Screening hits were confirmed by 3H-isoleucine incorporation. Of 43 targets screened, siRNA-mediated depletion of Fbxo6, Fbxo45, and Fbxl14 resulted in decreased cell size, whereas depletion of Fbxo9, Fbxo25, Fbxo30, Fbxo32, Fbxo33, Cullin1, Roc1, Ddb1, Fbxw4, and Fbxw5 led to a markedly increased cell size under basal conditions. In CM stimulated with phenylephrine (PE), depletion of Fbxo6, Fbxo25, Fbxo33, Fbxo45, and Fbxw4 further augmented PE-induced hypertrophy. As a proof-of-concept, the CRLFbox25 was analysed by transverse aortic constriction (TAC) resulting in a 4.5-fold increase in Fbxo25 protein concentrations compared to control animals. In cell culture, siRNA-mediated depletion of Fbxo25 resulted in a ∼ 37% increase in CM cell size and ∼41% increase in 3H-isoleucine incorporation. Depleting Fbxo25 resulted in upregulation of Anp and Bnp. In summary, we identified 13 novel CRLs as positive or negative regulators of CM hypertrophy. Of these, CRLFbox25 was further characterized, as a potential modulator of cardiac hypertrophy.
| S-EPMC10030680 | biostudies-literature
Project description:The cullin-RING ubiquitin E3 ligase (CRL) family consists of ~250 complexes that catalyze ubiquitylation of proteins to achieve cellular regulation. All CRLs are inhibited by the COP9 signalosome complex (CSN) through both enzymatic (deneddylation) and nonenzymatic (steric) mechanisms. The relative contribution of these two mechanisms is unclear. Here, we decouple the mechanisms using CSNAP, the recently discovered ninth subunit of the CSN. We find that CSNAP reduces the affinity of CSN toward CRL complexes. Removing CSNAP does not affect deneddylation, but leads to global effects on the CRL, causing altered reproductive capacity, suppressed DNA damage response, and delayed cell cycle progression. Thus, although CSNAP is only 2% of the CSN mass, it plays a critical role in the steric regulation of CRLs by the CSN.
| S-EPMC7206152 | biostudies-literature
Project description:Viruses have an ambivalent relationship with the host proteome. While several host proteins are indispensable for replication, detrimental restriction factors need to be antagonized. This process is frequently catalysed by viral accessory proteins which exploit the ubiquitin proteasome pathway, DDB1, and Cullin Ubiquitin ligases for the degradation of restriction factors, like in the case of the mouse cytomegalovirus encoded interferon antagonist pM27 which exploits DDB1 for STAT2 degradation. pM27 homologous proteins are conserved in betaherpesviruses. DDB1 and Cullins also serve as essential co-factor for accessory proteins encoded by other virus families like Vpr (HIV-1- and -2-encoded), Vpx (HIV-2-encoded), HBx (HBV-encoded) and its woodchuck hepatitis virus homolog (WHx). To establish a comprehensive understanding of the complexes assembled by viral DDB1-interacting proteins and their targets, we performed immuno-affinity precipitations for a panel of viral proteins known or suspected to interact with DDB1 and/or Cullins. For each protein, we conducted four biological replicates and identified and quantified all co-precipitating proteins by mass spectrometry. Empty plasmids and the HCMV-encoded protein pUL42, which binds the unrelated ubiquitin ligase Itch, served as negative controls and outside group, respectively. This analysis confirmed previously described interactions (pM27 with STAT2), extended known interactions to paralogous proteins (e.g. HBx and WHx with different Spindlin proteins), and documented anticipated interactions for the first time (e.g. Vpr with Bax). The comparison revealed considerable differences concerning the interaction with DDB1 and Cullin 4A/B in terms of the general ability as well as the strength of interaction. On global level, the correlation of the interactomes fitted well with the phylogenetic relationship of the proteins but also highlighted a considerable overlap between the DDB1 interactors of non-related viruses (e.g. herpesviral and hepadnaviral).
2019-01-14 | PXD007634 | Pride