RNA-sequencing facilitates Quantitative Analysis of Wild Type and Tsg101 Transgenic cardiac transcriptomes
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE126653 | GEO | 2019/02/27
REPOSITORIES: GEO
Similar Datasets
Project description:Abscission is the final stage of cytokinesis whereby the midbody, a thin intercellular bridge, is resolved to separate the daughter cells. Cytokinetic abscission is mediated by the Endosomal Sorting Complex Required for Transport (ESCRT), a conserved membrane remodelling machinery. The midbody organiser CEP55 recruits early acting ESCRT factors such as ESCRT-I and ALIX, which subsequently initiate the formation of ESCRT-III polymers that sever the midbody. We now identify UMAD1 as an ESCRT-I subunit that facilitates abscission. UMAD1 selectively associates with VPS37C and VPS37B, supporting the formation of cytokinesis-specific ESCRT-I assemblies. TSG101 recruits UMAD1 to the site of midbody abscission, to stabilise the CEP55/ESCRT-I interaction. We further demonstrate that the UMAD1/ESCRT-I interaction facilitates the final step of cytokinesis. Paradoxically, UMAD1 and ALIX co-depletion has synergistic effects on abscission whilst ESCRT-III recruitment to the midbody is not inhibited. Importantly, we find that both UMAD1 and ALIX are required for the dynamic exchange of ESCRT-III subunits at the midbody. Therefore, UMAD1 reveals a key functional connection between ESCRT-I and ESCRT-III that is required for cytokinesis.
2023-08-04 | PXD043940 | Pride
Project description:Cytokinesis requires the constriction of ESCRT-III filaments on the midbody side, where abscission occurs. After ESCRT recruitment at the midbody, it is not known how the ESCRT-III machinery localizes to the abscission site. We obtained the proteome of intact, post-abscission midbodies (Flemmingsome) and revealed enriched proteins in this organelle. We propose that the ESCRT-III machinery must be physically coupled to a membrane protein at the cytokinetic abscission site for productive scission, revealing novel common requirements in cytokinesis, exosome formation and retroviral budding.
2020-05-22 | PXD013219 | Pride
Project description:The proteasome is central to proteolysis by the ubiquitin-proteasome system under normal growth conditions but is itself degraded through macroautophagy under nutrient stress. A recently described AMPactivated protein kinase (AMPK)-regulated endosomal sorting complex required for transport (ESCRT)-dependent microautophagy pathway also regulates proteasome trafficking and degradation in low-glucose conditions in yeast. Aberrant proteasomes are more prone to microautophagy, suggesting the ESCRT system fine-tunes proteasome quality control under low-glucose stress. Here, we uncover additional features of the selective microautophagy of proteasomes in budding yeast. Genetic or pharmacological induction of aberrant proteasomes is associated with increased mono- or oligo-ubiquitylation of proteasome components, which appears to be recognized by ESCRT-0. AMPK controls this pathway in part by regulating the trafficking of ESCRT-0 to the vacuole surface, which also leads to degradation of the Vps27 subunit of ESCRT-0. The Rsp5 ubiquitin ligase contributes to proteasome subunit ubiquitylation, and multiple ubiquitin-binding elements in Vps27 are involved in their recognition.We propose that ESCRT-0 at the vacuole surface recognizes ubiquitylated proteasomes and initiates their microautophagic elimination during glucose depletion.
2022-02-06 | PXD031469 |
Project description:Ample evidence points to the contribution of endocytosis to oncogenesis at the cellular level but molecular details still remain obscure. Our analysis of The Cancer Genome Atlas data involving cohorts of colorectal cancer (CRC) patients revealed stage-dependent alterations in the expression of 113 genes whose function is related to endocytic transport. Among differentially expressed genes we observed decreased transcription of VPS37B and to a lesser extent VPS37A in the advanced stages of CRC. One member of the Vps37 protein family (Vps37A, Vps37B, Vps37C, Vps37D) together with Tsg101 and Vps28 forms the core of the Endosomal Sorting Complex Required for Transport (ESCRT)-I mediating membrane-remodeling processes. Our analysis of an independent cohort of CRC patients corroborated that both VPS37B and VPS37A genes are downregulated at mRNA and protein levels. Depletion of both Vps37A and Vps37B proteins elicits multifaceted transcriptional alterations, including cell growth arrest and induction of sterile inflammatory response, which are further potentiated by co-silencing of VPS37C. Among analyzed silencing condition, concurrent knockdown of VPS37A, VPS37B and VPS37C evokes the greatest magnitude of p21-mediated inhibition of cell proliferation and activation of Nuclear Factor-κB and mitogen-activated protein kinases signaling. These processes are independently induced after co-silencing of VPS37 paralogs. We further show that the type and magnitude of transcriptional responses correlate with the ESCRT-I stability, which is differentially affected upon individual and concurrent Vps37 depletion. Our study provides novel insights into cancer cell biology by describing a cellular stress response that is associated with ESCRT-I destabilization, which might occur in CRC patients
2020-12-17 | GSE152195 | GEO
Project description:Stimulator of interferon genes (STING) is essential for the type I interferon response against a variety of DNA pathogens. Upon emergence of cytosolic DNA, STING translocates from the endoplasmic reticulum (ER) to the Golgi where STING activates the downstream kinase TBK1, then to lysosome through recycling endosomes (REs) for its degradation. Although the molecular machinery of STING activation is extensively studied and defined, the one underlying STING degradation and inactivation has not yet been fully elucidated. Here we show that STING is degraded by the endosomal sorting complexes required for transport (ESCRT)-driven microautophagy. Airyscan super-resolution microscopy and correlative light/electron microscopy suggest that STING-positive vesicles of an RE origin are directly encapsulated into Lamp1-positive compartments. Screening of mammalian Vps genes, the yeast homologues of which regulate Golgi-to-vacuole transport, shows that ESCRT proteins are essential for the STING encapsulation into Lamp1-positive compartments. Knockdown of Tsg101 and Vps4, components of ESCRT, results in the accumulation of STING vesicles in the cytosol, leading to the sustained type I interferon response. Knockdown of Tsg101 in human primary T cells leads to an increase the expression of interferon-stimulated genes. STING undergoes K63-linked ubiquitination at lysine 288 during its transit through the Golgi/REs, and this ubiquitination is required for STING degradation. Our results reveal a molecular mechanism that prevents hyperactivation of innate immune signalling, which operates at REs.
2023-01-24 | PXD039411 | Pride
Project description:Endosomal trafficking plays an integral role in various eukaryotic cell activities. In animal cells, a member of the RAB GTPase family, RAB5, is known as a key regulator of various endosomal functions, which include endosomal fusion, endosomal signaling, and endosomal motility. In addition to orthologs of animal RAB5, plants harbor the plant-unique RAB5 group, ARA6 group, which is conserved in all land plant lineages. The Arabidopsis genome encodes three RAB5 members: two conventional type RAB5 (ARA7 and RHA1) and one plant-specific ARA6. It has been already reported that ARA6 mediates a trafficking pathway from endosomes to the plasma membrane, and also shown to be involved in salt stress tolerance and flowering. However, physiological functions of ARA6 and their detailed mechanism are still remained elusive. In this study, we carried out a microarray analysis of the ara6-1 mutant. Possible involvement of ARA6 in sugar metabolism will be reported. The transcriptional profiling between the wild-type Col. and a RAB5 knock out mutant, ara6-1.
2015-02-18 | E-GEOD-57013 | biostudies-arrayexpress
Project description:Cell death plasticity is crucial for modulating tissue homeostasis and immune responses, but our understanding of the molecular components that regulate cell death pathways to determine cell fate remains limited. Here, a CRISPR screen of acute myeloid leukemia cells identifies protein tyrosine phosphatase non-receptor type 23 (PTPN23) as essential for survival. Loss of PTPN23 activates nuclear factor-kappa B, apoptotic, necroptotic, and pyroptotic pathways by causing the accumulation of death receptors and toll-like receptors (TLRs) in endosomes. These effects are recapitulated by depletion of PTPN23 co-dependent genes in the endosomal sorting complex required for transport (ESCRT) pathway. Through proximity-dependent biotin labeling, we show that NAK-associated protein 1 interacts with PTPN23 to facilitate endosomal sorting of tumor necrosis factor receptor 1 (TNFR1), sensitizing cells to TNF-alpha-induced cytotoxicity. Our findings reveal PTPN23-dependent ESCRT machinery as a cell death checkpoint that regulates the spatiotemporal distribution of death receptors and TLRs to restrain multiple cell death pathways.
2024-10-16 | GSE272123 | GEO
Project description:ATG9 is often described as the sole transmembrane protein among the core
autophagy factors. The mammalian ATG9A is notorious for trafficking through
numerous cellular compartments including the plasma membrane. The
reasons for ATG9As wide intracellular distribution and its role at the PM are not
fully understood. Here we show that ATG9A intimately interacts with components
of the ESCRT system. Employing proteomic analyses with APEX2-ATG9A we
identified a number of ESCRTs as ATG9A interactors, including TSG101 and
ALIX, and uncovered cooperation between ATG9A and ESCRTs in protection
against PM damage. ATG9A knockouts sensitized PM to permeabilization by a
broad spectrum of agents including gasdermin and Mycobacterium tuberculosis.
ESCRTs phenocopied ATG9A in protection against PM injury. Thus, in addition
to its function in autophagy, ATG9A is a component of the ESCRT system
engaged in the repair of PM
2019-10-30 | MSV000084519 | MassIVE
Project description:Trafficking of G protein-coupled receptors (GPCRs) through the endo-lysosomal pathway is critical to homeostatic regulation of GPCRs following activation with agonist. Identifying the genes involved in GPCR trafficking is challenging due to the complexity of sorting operations and low affinity protein-receptor interactions. Here we show that the engineered enzyme APEX2 is a highly sensitive biosensor for GPCR trafficking to the lysosome, and this trafficking can be monitored through APEX-based activation of fluorogenic substrates such as Amplex UltraRed (AUR). We used GPCR-APEX2/AUR to perform a genome-wide CRISPR interference screen focused on the delta type opioid receptor (DOR), a GPCR which modulates anxiety and pain. We provide a genetic map of components in the endo-lysosomal pathway necessary for DOR trafficking to the lysosome and subsequent downregulation. Using our GPCR-APEX2 pipeline, we demonstrate that a gene identified in our screen, DNAJC13, controls trafficking of DOR to the lysosome by regulating the endosomal proteome and endosomal homeostasis.
2024-07-01 | GSE242366 | GEO
Project description:The functions of integrins are tightly regulated via multiple mechanisms including trafficking and degradation. Integrins are repeatedly internalized, routed into the endosomal system and either degraded by the lysosome or recycled back to the plasma membrane. The ubiquitin system dictates whether internalized proteins are degraded or recycled. Here, we used a genetic screen and proximity-dependent biotin identification to identify deubiquitinase(s) that control integrin surface levels. We found that a ternary deubiquitinating complex, comprised of USP12 (or the homologous USP46), WDR48 and WDR20, stabilizes β1 integrin (Itgb1) by preventing ESCRT-mediated lysosomal degradation. Mechanistically, the USP12/46-WDR48-WDR20 complex removes ubiquitin from the cytoplasmic tail of internalized Itgb1 in early endosomes, which in turn prevents ESCRT-mediated sorting and Itgb1 degradation.
2024-09-06 | PXD054760 | Pride