Changes of mRNA expressin in rat kidney inner medulla in response to dDAVP stimulation/ withdrawal
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE27449 | GEO | 2011/02/23
SECONDARY ACCESSION(S): PRJNA137061
REPOSITORIES: GEO
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Project description:The E3 ubiquitin -protein ligases (E3s) plays a role as regulators of protein trafficking and degradation. We aimed to identify E3s in rat kidney which are associated with dDAVP-induced urine concentration. Kidney inner medulla collected from vehicle treated control (n=2), dDAVP infusion for 5 d (D5d, n=2) and 3 h-withdrawal of dDAVP after 5 d-infusion (D5d-3h, n=2) groups were subjected to a transcriptome analysis.
2011-02-23 | E-GEOD-27449 | biostudies-arrayexpress
Project description:Activation of the renal urine concentrating mechanism by vasopressin requires the coordinated regulation of multiple gene products including ion transporters, and water channels as well as regulatory proteins like protein kinases and phosphatases or enzymes involved in the energy-metabolism of the cells. We used microarray analysis of AVP-regulated gene products in a rat model of central diabetes insipidus (DI) to generate a comprehensive database documenting these changes. For microarray studies young (8 weeks) adult male Brattleboro rats were randomly divided into 2 groups (n = 3 per group) and treated for 3 days with either 1-desamino-8-D-Arg vasopressin (dDAVP; 5ng/h; Sigma Aldrich, Germany) or vehicle via osmotic minipump (ALZET minipump model 2001, Charles River, Sulzfeld, Germany). At the end of the treatment period animals were sacrificed and the kidneys removed. The outer medulla was isolated and used for cDNA generation and subsequent microarray analysis using [Rat230_2] Affymetrix Rat Genome 230 2.0 Array.
2012-03-01 | E-GEOD-34225 | biostudies-arrayexpress
Project description:The post-translational modification of proteins by ubiquitination is a highly regulated process that involves a dynamic, three-step enzymatic cascade, where more than 600 E3 ligases play a critical role in recognizing specific substrates for modification. Separating bona fide targets of E3s from E3-interacting proteins remains a major challenge in the field. In this study, we present BioE3, a novel approach for identifying substrates of ubiquitin-like (UbL) E3 ligases of interest. Using BirA-E3 ligase fusion proteins and bioUbLs, the method facilitates site-specific biotinylation of UbL-modified substrates for proteomic identification. We demonstrate that the BioE3 system can identify both known and novel targets of two RING-type ubiquitin E3 ligases: RNF4, known to be involved in DNA damage response and the regulation of PML nuclear bodies, and MIB1, implicated in endocytosis, autophagy, and centrosomal protein homeostasis. We further show the versatility of BioE3 by identifying targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, we show that BioE3 works with HECT-type E3 ligases and identify novel targets of NEDD4 involved in vesicular trafficking. BioE3 is a powerful tool that enables identification of bona fide substrates of UbL E3 ligases and how they change with chemical perturbations, which may be useful for the emerging applications in targeted protein degradation (TPD). BioE3 may also be applicable for UbLs beyond Ub and SUMO, as well as other E3 ligase classes. The resulting knowledge can shed light on the regulation of cellular processes by the complex UbL network, advancing our understanding of fundamental biological mechanisms.
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Project description:Ubiquitin ligases (E3s) serves as a key regulator for ubiquitylation-mediated pathway. The identification of the corresponding relationship between E3 and its substrates is challenging but required for understanding the regulatory network of ubiquitylation. The low abundance of ubiquitinated conjugates and high redundancy of E3s-substrates regulation made screening pretty hard. Herein, we combined SILAC-based quantitative proteomics with two contrary genetic methods (overexpression and knockout) in theory for E3 (Hrt3, F-box subunit of SCF complex) substrates screening.
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Project description:Neddylation is necessary for activation of Cullin-RING Ligases (CRLs) which degrade various immune regulatory proteins. Our recent study showed that while depletion of neddylation E2-E3 pair Ube2f-Sag in regulatory T cells (Treg cells) had no obvious phenotype, the same depletion of either Ube2m or Rbx1 caused inflammation disorders with different severity. Whether these E2s or E3s compensate each other in functional regulations of Treg cells is, however, previously unknown. In this report, we generated Foxp3Cre;Ube2mfl/fl;Ube2ffl/fl or Foxp3Cre;Rbx1fl/fl;Sagfl/fl double null mice by simultaneously deletion of both neddylation E2s or E3s in Treg cells, respectively. Remarkably, Ube2m&Ube2f double null mice developed much severe autoimmune phenotypes than Ube2m-null mice, indicating Ube2m significantly compensates Ube2f in Treg cells. The minor worsen autoimmune phenotypes seen at very early stage in Rbx1&Sag double null than Rbx1-null mice, is likely due to already severe phenotypes of the later, indicating a minor compensation of Rbx1 for Sag. The RNA profiling-based analyses revealed that up- and down-regulations of few signaling pathways in Treg cells are associated with the severity of autoimmune phenotypes. Finally, severer inflammation phenotypes seen in mice with double E3-null than with double E2-null Treg cells indicate a neddylation-independent mechanism of two E3s, also known to serve as the RING component of CRLs in regulation of Treg cell fitness.
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Project description:Neddylation is necessary for activation of Cullin-RING Ligases (CRLs) which degrade various immune regulatory proteins. Our recent study showed that while depletion of neddylation E2-E3 pair Ube2f-Sag in regulatory T cells (Treg cells) had no obvious phenotype, the same depletion of either Ube2m or Rbx1 caused inflammation disorders with different severity. Whether these E2s or E3s compensate each other in functional regulations of Treg cells is, however, previously unknown. In this report, we generated Foxp3Cre;Ube2mfl/fl;Ube2ffl/fl or Foxp3Cre;Rbx1fl/fl;Sagfl/fl double null mice by simultaneously deletion of both neddylation E2s or E3s in Treg cells, respectively. Remarkably, Ube2m&Ube2f double null mice developed much severe autoimmune phenotypes than Ube2m-null mice, indicating Ube2m significantly compensates Ube2f in Treg cells. The minor worsen autoimmune phenotypes seen at very early stage in Rbx1&Sag double null than Rbx1-null mice, is likely due to already severe phenotypes of the later, indicating a minor compensation of Rbx1 for Sag. The RNA profiling-based analyses revealed that up- and down-regulations of few signaling pathways in Treg cells are associated with the severity of autoimmune phenotypes. Finally, severer inflammation phenotypes seen in mice with double E3-null than with double E2-null Treg cells indicate a neddylation-independent mechanism of two E3s, also known to serve as the RING component of CRLs in regulation of Treg cell fitness.
2023-08-12 | GSE237497 | GEO
Project description:Ubiquitin and ubiquitin-like conjugation cascades consist of dedicated E1, E2 and E3 enzymes with E3s providing substrate specificity. Mass spectrometry-based approaches have enabled the identification of more than 60,000 acceptor sites for ubiquitin and 40,000 acceptor sites for SUMO2/3. However, E3-to-target wiring is poorly understood. The limited number of SUMO E3s provides the unique opportunity to systematically study E3-substrate wiring. We developed SUMO Activated Target Traps (SATTs) and, in the presence of proteasome inhibitor MG132,systematically identified substrates for eight different SUMO E3s, PIAS1, PIAS2, PIAS3, PIAS4, NSMCE2, ZNF451, LAZSUL(ZNF451-3) and ZMIZ2. SATTs enabled us to identify 427 SUMO1 and 961 SUMO2/3 targets in an E3-specific manner. We found pronounced E3 substrate preference, even at the substrate isoform level. Quantitative proteomics enabled us to measure substrate specificity of E3s, quantified using the SATT index. Furthermore, we developed the Polar SATTs web-based tool (https://amsterdamstudygroup.shinyapps.io/polarVolcaNoseR_revised/) to browse the dataset in an interactive manner, increasing the accessibility of this resource for the community. Overall, we uncover E3-to-target wiring of 1388 SUMO substrates, highlighting unique and overlapping sets of substrates for eight different SUMO E3 ligases.
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Project description:Vasopressin, the antidiuretic hormone, acts on the renal collecting duct. In this experiment both vasopressin (AVP) and the V2R specific agonist dDAVP were infused into Aquaporin 1 knockout animals for 7 days. The aim of the experiment was to identify genes increased by vasopressin receptors in the renal medullary collecting ducts, in the absence of an increase in renal medullary osmolarity (the AQP1 knockouts are concentrating mechanism knockouts). All experiments used inner medulla tissue for the RNA isolation. Hybridizations were performed that compared kidney inner medulla total RNA from three control mice against kidney medulla total RNA from 3 mice infused with either arginine vasopressin (AVP) or des-amino-D-arginine vasopressin (dDAVP).
2007-10-06 | E-GEOD-5953 | biostudies-arrayexpress
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Project description:Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 different stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
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