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Endocytosis: the DUB version
Abstract
Dynamic modification of endosomal cargo proteins, such as the epidermal growth factor receptor, by ubiquitin can regulate their sorting into the lumen of multivesicular bodies through interactions with a complex protein network incorporating the endosomal sorting complexes required for transport (ESCRTs). Two deubiquitinating enzymes, AMSH and UBPY, interact with ESCRT protein components but exert opposite effects upon the rate of epidermal growth factor receptor downregulation. This might reflect their distinct specificities for different types of polyubiquitin chain linkage. We propose that AMSH might rescue ubiquitinated cargo from lysosomal degradation through disassembly of K63-linked polyubiquitin chains. UBPY function is essential for effective downregulation but is likely to be multifaceted, encompassing activity against both K63-linked and K48-linked polyubiquitin chains and including regulation of the stability of ESCRT-associated proteins such as STAM, by reversing their ubiquitination.
... Typically, the endocytic trafficking process involves the internalization, endosomal sorting, and lysosomal degradation of cell-surface receptors and is strictly executed by the endosomal sorting complexes required for transport (ESCRT), consisting of at least five macromolecular assemblies termed ESCRT-0, ESCRT-I, ESCRT-II, and ESCRT-III and vacuolar sorting protein 4 (Vps4) [54][55][56]. It is during this process that AMSH can interact with the components ESCRT-0 and ESCRT-III and so affect the fate of receptors [16]. ...
... Interestingly, AMSH has a close homolog AMSH-LP (AMSH-like protein) [35]. Although the entire amino acid sequences of AMSH and AMSH-LP are only 54% identical, their three-dimensional structures exhibit extremely high similarity [16,26]. Especially, their catalytic domains and residues involved in proximal ubiquitin recognition are completely conserved [50,84]. ...
... However, AMSH-LP lacks several key features and presents some significant differences in the residues used for interaction with the distal ubiquitin [85]. Besides, AMSH contains an SBM domain, which interacts with the STAM of ESCRT-0 while a functional SBM is lost in human AMSH-LP [16]. By further exploring the differences in the properties, Davies et al. found that the catalytic domain of AMSH was thermodynamically less stable than that of AMSH-LP. ...
Deubiquitinating enzymes (DUBs) are a group of proteases that are important for maintaining cell homeostasis by regulating the balance between ubiquitination and deubiquitination. As the only known metalloproteinase family of DUBs, JAB1/MPN/Mov34 metalloenzymes (JAMMs) are specifically associated with tumorigenesis and immunological and inflammatory diseases at multiple levels. The far smaller numbers and distinct catalytic mechanism of JAMMs render them attractive drug targets. Currently, several JAMM inhibitors have been successfully developed and have shown promising therapeutic efficacy. To gain greater insight into JAMMs, in this review, we focus on several key proteins in this family, including AMSH, AMSH-LP, BRCC36, Rpn11, and CSN5, and emphatically discuss their structural basis, diverse functions, catalytic mechanism, and current reported inhibitors targeting JAMMs. These advances set the stage for the exploitation of JAMMs as a target for the treatment of various diseases.
... K48-linked ubiquitin chains are most common and target proteins for degradation via the ubiquitin proteasome pathway [9]. K63-linked ubiquitination, the second most common ubiquitin chain type, carries signals essential for DNA repair, the stress and immune response, and membrane protein homeostasis [10,11]. ...
... Membrane proteins are degraded via the endosomal-lysosomal pathway: Targets for degradation are marked with K63-linked ubiquitin chains, which are recognized by the endosomal sorting complexes, which in turn deliver the target to the lysosome where it is degraded. The abundance of membrane receptors is regulated by a tug-of-war between E3 ligases that deposit degradation signals and DUBs that remove the degradation signals and thereby rescue the membrane proteins from degradation [11]. Similar to other DUBs that counteract degradation of specific membrane proteins (e.g., AMSH rescuing EGFR [11]) BRISC counteracts ubiquitination of IFNAR1 and the HIV-1 Tat protein [67,68]. ...
... The abundance of membrane receptors is regulated by a tug-of-war between E3 ligases that deposit degradation signals and DUBs that remove the degradation signals and thereby rescue the membrane proteins from degradation [11]. Similar to other DUBs that counteract degradation of specific membrane proteins (e.g., AMSH rescuing EGFR [11]) BRISC counteracts ubiquitination of IFNAR1 and the HIV-1 Tat protein [67,68]. ...
The K63-linkage specific deubiquitinase BRCC36 forms the core of two multi-subunit deubiquitination complexes: BRCA1-A and BRISC. BRCA1-A is recruited to DNA repair foci, edits ubiquitin signals on chromatin, and sequesters BRCA1 away from the site of damage, suppressing homologous recombination by limiting resection. BRISC forms a complex with metabolic enzyme SHMT2 and regulates the immune response, mitosis, and hematopoiesis. Almost two decades of research have revealed how BRCA1-A and BRISC use the same core of subunits to perform very distinct biological tasks.
... The receptors are then incorporated into luminal vesicles of multi-vesicular bodies (MVBs) before fusion with lysosomes (Futter et al., 1996). Two endosomal deubiquitylating enzymes (DUBs), USP8 (UBPY) and AMSH (associated molecule with the SH3 domain of STAM; STAM binding protein, STAMBP), interact with the ESCRT machinery and can differentially influence the fate of endocytosed receptors Clague and Urbe, 2006). It is known that CTLA4 can be ubiquitylated, but not whether this ubiquitylation influences endosomal sorting. ...
... It is The copyright holder for this preprint this version posted January 1, 2024. ; https://doi.org/10.1101/2023.12.31.573735 doi: bioRxiv preprint stability, despite their sharing of many interactions Clague and Urbe, 2006). AMSH will not cleave a proximal ubiquitin and we here provide evidence for a significant population of dual mono-ubiquitylated CTLA4, which provides a relatively weak endosomal sorting signal for other receptor types (Haglund et al., 2003;Ma et al., 2012). ...
The immune checkpoint regulator CTLA4 is an unusually short-lived membrane protein. Here we show that its lysosomal degradation is dependent on ubiquitylation at Lysine residues 203 and 213. Inhibition of the v-ATPase partially restores CTLA4 levels following cycloheximide treatment, but also reveals a fraction that is secreted in exosomes. The endosomal deubiquitylase, USP8, interacts with CTLA4 and its loss enhances CTLA4 ubiquitylation in cancer cells, mouse CD4+ T cells and in cancer cell-derived exosomes. Depletion of the USP8 adapter protein, HD-PTP, but not ESCRT-0 recapitulates this cellular phenotype, but shows distinct properties vis-a-vis exosome incorporation. Re-expression of wild-type USP8, but neither a catalytically inactive, nor a localisation-compromised ΔMIT domain mutant can rescue delayed degradation of CTLA4, or counteract its accumulation in clustered endosomes. UbiCRest analysis of CTLA4-associated ubiquitin chain linkages identifies a complex mixture of conventional Lys63- and more unusual Lys27- and Lys29-linked polyubiquitin chains that may underly the rapidity of protein turnover.
... While the other six families of human DUBs are cysteine proteases, the JAMM family is unique in that they are metalloproteases. The JAMM domain (17) contains a catalytic zinc ion coordinated by two histidines, one aspartate/glutamate, and one water molecule that is hydrogen-bonded to an adjacent glutamate (18). The JAMM family comprises a total of 14 DUBs, seven of which are predicted to be catalytically inactive (pseudo-DUBs) because of substitutions of essential Zn 2+ -coordinating residues (19). ...
... STAMBP plays an essential role in endocytosis and endosomal-lysosomal sorting of cell-surface receptors by deubiquitinating and rescuing ubiquitinated cargo proteins from lysosomal degradation. The MIT and SBM domains mediate critical protein-protein interactions (17) to recruit STAMBP to the endosomal sorting complexes required for transport (ESCRT), which regulate the multivesicular body (MVB) biogenesis of ubiquitinated cellreceptors (27). Recessive mutations in the STAMBP gene were found to cause a severe developmental disorder, microcephaly capillary malformation syndrome (MIC-CAP), due to elevated Ub-conjugate aggregation and resulted progressive apoptosis (28). ...
Ubiquitination is a crucial post-translational protein modification involved in a myriad of biological pathways. This modification is reversed by deubiquitinases (DUBs) that deconjugate the single ubiquitin (Ub) moiety or poly-Ub chains from substrates. In the past decade, tremendous efforts have been focused on targeting DUBs for drug discovery. However, most chemical compounds with inhibitory activity for DUBs suffer from mild potency and low selectivity. To overcome these obstacles, we developed a phage display-based protein engineering strategy for generating Ub variant (UbV) inhibitors, which was previously successfully applied it to the Ub-specific protease (USP) family of cysteine proteases. In this work, we leveraged the UbV platform to selectively target STAMBP, a member of the JAB1/MPN/MOV34 (JAMM) metalloprotease family of DUB enzymes. We identified two UbVs (UbVSP.1 and UbVSP.3) that bind to STAMBP with high affinity but differ in their selectivity for the closely related paralog STAMBPL1. We determined the STAMBPL1-UbVSP.1 complex structure by X-ray crystallography, revealing hotspots of the JAMM-UbV interaction. Finally, we show that UbVSP.1 and UbVSP.3 are potent inhibitors of STAMBP isopeptidase activity, far exceeding the reported small-molecule inhibitor BC-1471. This work demonstrates that UbV technology is suitable to develop molecules as tools to target metalloproteases which can be used to further understand the cellular function of JAMM family DUBs.
... While the other six families of human DUBs are cysteine proteases, the JAMM family is unique in that they are metalloproteases. The JAMM domain (17) contains a catalytic zinc ion coordinated by two histidines, one aspartate/glutamate, and one water molecule that is hydrogen-bonded to an adjacent glutamate (18). The JAMM family comprises a total of 14 DUBs, seven of which are predicted to be catalytically inactive (pseudo-DUBs) because of substitutions of essential Zn 2+ -coordinating residues (19). ...
... STAMBP plays an essential role in endocytosis and endosomal-lysosomal sorting of cell-surface receptors by deubiquitinating and rescuing ubiquitinated cargo proteins from lysosomal degradation. The MIT and SBM domains mediate critical protein-protein interactions (17) to recruit STAMBP to the endosomal sorting complexes required for transport (ESCRT), which regulate the multivesicular body (MVB) biogenesis of ubiquitinated cellreceptors (27). Recessive mutations in the STAMBP gene were found to cause a severe developmental disorder, microcephaly capillary malformation syndrome (MIC-CAP), due to elevated Ub-conjugate aggregation and resulted progressive apoptosis (28). ...
Ubiquitination is one of the most crucial post-translational protein modifications involved in a myriad of biological pathways. This process is reversed by deubiquitinases (DUBs) that deconjugate the ubiquitin (Ub) moiety or poly-Ub chains from substrates. In the past decade, tremendous efforts have been focused on targeting DUBs for drug discovery. However, most chemical compounds with inhibitory activity for DUBs suffer from mild potency and low selectivity. To overcome these obstacles, we developed a phage display-based protein engineering strategy for generating Ub variant (UbV) inhibitors and have previously successfully applied it to the Ub-specific protease (USP) family of cysteine proteases. In this work, we leveraged the UbV platform to target STAMBP, a member of the JAB1/MPN/MOV34 (JAMM) metalloprotease family of DUB enzymes. We identified two UbVs (UbV SP.1 and UbV SP.3 ) that bind to STAMBP with high affinity but differ in their selectivity for the closely related paralog STAMBPL1. We determined the STAMBPL1-UbVSP.1 complex structure by X-ray crystallography, revealing hotspots of the tight JAMM-UbV interaction. Finally, we show that UbV SP.1 and UbV SP.3 are potent inhibitors of the STAMBP isopeptidase activity, far exceeding the reported small-molecule inhibitor BC-1471. This work demonstrates the UbV technology is suitable to develop tool molecules for metalloproteases. These tools can be used to understand the cellular function of JAMM family DUBs.
... A variety of disease-causing mutations have been identified including frameshift, nonsense, splicing, and missense mutations, implicating loss-of-function as a mechanism of disease [146,[180][181][182][183]. Indeed, Amsh-deficient mice exhibit defects in cortical development similar to those in patients [39]. AMSH is a DUB that, through its K63-specific ubiquitin cleavage activity [184], controls the fate of endosomal cargos that undergo ubiquitin-dependent sorting into degradation or recycling compartments by the ESCRT pathway [65,185]. The reported disease-causing missense mutations in AMSH are located either in the catalytic domain reducing its K63-cleavage activity [186] or in the MIT domain potentially affecting binding to components of the ESCRT pathway [146,185]. ...
... AMSH is a DUB that, through its K63-specific ubiquitin cleavage activity [184], controls the fate of endosomal cargos that undergo ubiquitin-dependent sorting into degradation or recycling compartments by the ESCRT pathway [65,185]. The reported disease-causing missense mutations in AMSH are located either in the catalytic domain reducing its K63-cleavage activity [186] or in the MIT domain potentially affecting binding to components of the ESCRT pathway [146,185]. During the pathogenesis of MIC-CAP, dysregulation of endosomal sorting likely interferes with appropriate responses to downregulate RAS/PI3K signaling, ultimately leading to the congenital anomalies observed in patients. ...
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate’s stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
... De novo ubiquitin is liberated from these fusions by the action of deubiquitinating enzymes (DUBs) such as USP5 and Otulin (Falquet et al. 1995;Grou et al. 2015). DUBs can also control free ubiquitin levels by limiting the entry of ubiquitin into either the proteasome or lysosome (Clague and Urbe 2006;Singhal et al. 2008;Finley 2009;Reyes-Turcu et al. 2009;Shabek and Ciechanover 2010;Piper et al. 2014). Both ubiquitin C-terminal hydrolase L1 and USP14, which are thought to act upstream of proteasomal and lysosomal protein degradation, have been implicated in maintaining ubiquitin pools in neurons, and loss-of-function mutations in either of these DUBs cause abnormalities in synaptic structure and function (Chen et al. 2009(Chen et al. , 2010Genc et al. 2016). ...
... The endosomal sorting complex required for transport (ESCRT) is a second ubiquitin-dependent pathway that directs ubiquitinated proteins to the lysosome for degradation (Clague and Urbe 2006). The first two complexes in the ESCRT pathway, ESCRT-0 and ESCRT-I, both contain ubiquitin-binding proteins that are thought to capture and direct internalized ubiquitinated proteins to the lysosome. ...
Ubiquitin is an essential signaling protein that controls many different cellular processes. While cellular ubiquitin levels normally cycle between pools of free and conjugated ubiquitin, the balance of these ubiquitin pools can be shifted by exposure to a variety of cellular stresses. Altered ubiquitin pools are also observed in several neurological disorders, suggesting that imbalances in ubiquitin homeostasis may contribute to neuronal dysfunction. To examine the effects of increased ubiquitin levels on the mammalian nervous system, we generated transgenic mice that express ubiquitin under the control of the Thy1.2 promoter. While we did not detect global changes in levels of ubiquitin conjugates in the hippocampus, we found that increasing ubiquitin levels reduced AMPA (GRIA1‐4) receptor expression without affecting the levels of NMDA (GRIN) or GABAA receptors. Ubiquitin over‐expression also negatively impacted hippocampus‐dependent learning and memory as well as baseline excitability and synaptic plasticity at hippocampal CA3‐CA1 synapses. These changes occurred in a dose‐dependent manner in that mice with the highest levels of ubiquitin over‐expression had the greatest deficits in synaptic function and were the most impaired in the learning and memory tasks. As chronic elevation of ubiquitin expression in neurons is sufficient to cause changes in synaptic function and cognition, altered ubiquitin homeostasis may be an important contributor to the stress‐induced changes observed in neurological disorders.
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... AMSH is a metalloprotease of the JAMM type involved in the sorting of cell-surface receptors at endosomes [131][132][133][134]. AMSH localizes at the endosomes and promotes the recycling of internalized receptors [135,136]. Disruption of AMSH in mice results in the loss of neurons in the hippocampus and severe atrophy of the cerebral cortex [137]. An independent study observed that the loss of AMSH in neurons results in the accumulation of ubiquitinated protein aggregates associated with the autophagy receptor p62, indicating that the autophagy flux is impaired [138] ( Figure 3D). ...
... USP8 is a second DUB playing a major role in endocytosis by regulating both the ubiquitination status of cargoes and members of the ESCRT machinery regulating membrane deformation and scission events [126][127][128][140][141][142]. USP8 has been extensively studied for its role in the regulation of the trafficking and lysosomal degradation of receptors, such as EGFR, through the endocytic process [135,143]. In addition to its role in endocytosis, loss of dUSP8 in Drosophila blocks the progression of autophagy, resulting in the accumulation of Ref(2)P/p62 and ubiquitinated proteins [144]. ...
Autophagy is an evolutionary conserved catabolic process that allows for the degradation of intracellular components by lysosomes. This process can be triggered by nutrient deprivation, microbial infections or other challenges to promote cell survival under these stressed conditions. However, basal levels of autophagy are also crucial for the maintenance of proper cellular homeostasis by ensuring the selective removal of protein aggregates and dysfunctional organelles. A tight regulation of this process is essential for cellular survival and organismal health. Indeed, deregulation of autophagy is associated with a broad range of pathologies such as neuronal degeneration, inflammatory diseases, and cancer progression. Ubiquitination and deubiquitination of autophagy substrates, as well as components of the autophagic machinery, are critical regulatory mechanisms of autophagy. Here, we review the main evidence implicating deubiquitinating enzymes (DUBs) in the regulation of autophagy. We also discuss how they may constitute new therapeutic opportunities in the treatment of pathologies such as cancers, neurodegenerative diseases or infections.
... However, as these mutations have not been encountered in naturally-occurring P. falciparum, we cannot rule out a fitness deficit in vivo, and this may be due to additional roles for UBP-1 in liver, sexual or mosquito stages of the life cycle. DUB involvement in endocytosis has been described in higher eukaryotes, although these processes are notably distinct from the host cytosol ingestion of Plasmodium and, further, UBP-1 bears no resemblance to AMSH and UBPY, the mammalian enzymes involved (27). Of note, the Ub linkage preference profile of UBP-1 seems identical to that of UBPY (USP8) and more closely resembles that of other USP-type DUBs (manuscript submitted). ...
Deubiquitinating enzymes function to cleave ubiquitin moieties from modified proteins, serving to maintain the pool of free ubiquitin in the cell while simultaneously impacting the fate and function of a target protein. Like all eukaryotes, Plasmodium parasites rely on the dynamic addition and removal of ubiquitin for their own growth and survival. While humans possess around 100 DUBs, Plasmodium contains ~20 putative ubiquitin hydrolases, many of which bear little to no resemblance to those of other organisms. In this study, we characterize PfUBP-1, a large ubiquitin hydrolase unique to Plasmodium spp that has been linked to endocytosis and drug resistance. We demonstrate its ubiquitin activity, linkage specificity and assess the repercussions of point mutations associated with drug resistance on catalytic activity and parasite fitness.
... USP8/UBPY was identified to modulate TDP-43-induced neurotoxicity (Hans et al., 2014). This DUB was previously known to regulate endocytosis via interactions with ESCRT-associated protein components such as EGFRs or STAM (Clague and Urbé, 2006). By employing yeast two-hybrid screening and co-immunoprecipitation, Hans et al. revealed that UBPY is a novel interacting partner of pathogenic TDP-43. ...
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease in which motor neurons in spinal cord and motor cortex are progressively lost. About 15% cases of ALS also develop the frontotemporal dementia (FTD), in which the frontotemporal lobar degeneration (FTLD) occurs in the frontal and temporal lobes of the brain. Among the pathologic commonalities in ALS and FTD is ubiquitin-positive cytoplasmic aggregation of TDP-43 that may reflect both its loss-of-function and gain-of-toxicity from proteostasis impairment. Deep understanding of how protein quality control mechanisms regulate TDP-43 proteinopathies still remains elusive. Recently, a growing body of evidence indicates that ubiquitinating and deubiquitinating pathways are critically engaged in the fate decision of aberrant or pathological TDP-43 proteins. E3 ubiquitin ligases coupled with deubiquitinating enzymes may influence the TDP-43-associated proteotoxicity through diverse events, such as protein stability, translocation, and stress granule or inclusion formation. In this article, we recapitulate our current understanding of how ubiquitinating and deubiquitinating mechanisms can modulate TDP-43 protein quality and its pathogenic nature, thus shedding light on developing targeted therapies for ALS and FTD by harnessing protein degradation machinery.
... Our findings provide evidence that plant DUBs act in opposition during intracellular trafficking. In mammals, deubiquitination has been demonstrated to play a dual role in the regulation of intracellular trafficking (Clague & Urb e, 2006;Millard & Wood, 2006). DUBs facilitate endocytosis and vacuolar degradation of PM receptors by recruiting the components of clathrin-mediated endocytosis (Jaworski et al, 2014). ...
Protein ubiquitination is a dynamic and reversible post-translational modification that controls diverse cellular processes in eukaryotes. Ubiquitin-dependent internalization, recycling, and degradation are important mechanisms that regulate the activity and the abundance of plasma membrane (PM)-localized proteins. In plants, although several ubiquitin ligases are implicated in these processes, no deubiquitinating enzymes (DUBs), have been identified that directly remove ubiquitin from membrane proteins and limit their vacuolar degradation. Here, we discover two DUB proteins, UBP12 and UBP13, that directly target the PM-localized brassinosteroid (BR) receptor BR INSENSITIVE1 (BRI1) in Arabidopsis. BRI1 protein abundance is decreased in the ubp12i/ubp13 double mutant that displayed severe growth defects and reduced sensitivity to BRs. UBP13 directly interacts with and effectively removes K63-linked polyubiquitin chains from BRI1, thereby negatively modulating its vacuolar targeting and degradation. Our study reveals that UBP12 and UBP13 play crucial roles in governing BRI1 abundance and BR signaling activity to regulate plant growth.
... (ALK), and the PD-1/PD-L1 immune checkpoint axis are only applicable to a small proportion of lung cancer patients, and accordingly additional actionable therapeutic targets are in great request to design potential treatment modalities. The human deubiquitylases (DUBs) are a group of cysteine proteases and metalloenzymes that have been associated with a wide range of cellular activities including the dynamic regulation of cell surface receptors [35,36]. Endocytosis-associated deubiquitylases exemplified by AMSH, USP8, and USP2 have been shown to regulate the dynamic turnover of top therapeutic targets in cancer treatment such as EGFR and ErbB2/HER2 [14,29,37]. ...
Introduction
The human genome encodes two melatonin receptors (MT1 and MT2) that relay melatonin signals to cellular interior. Accumulating evidence has linked melatonin to multiple health benefits, among which its anticancer effects have become well-established. However, the implications of its receptors in lung adenocarcinoma have so far remained incompletely understood.
Objectives
This study aims to investigate the response of the MT1 receptor to melatonin treatment and its dynamic regulation by ubiquitin-specific protease 8 (USP8) in lung adenocarcinoma.
Methods
The mRNA levels of MT1 and MT2 receptors were analyzed with sequencing data. The expression and localization of the MT1 receptor with melatonin treatment were investigated by immunoblotting, immunofluorescence and confocal microscopy assays. Endocytic deubiquitylases were screened to identify MT1 association. The effects of USP8 were assessed with shRNA-mediated knockdown and small molecule inhibitor. The combined efficacy of melatonin and USP8 suppression was also evaluated using xenograft animal models.
Results
Bioinformatic analysis revealed increased expression of the MT1 receptor in lung adenocarcinoma tissues. Melatonin treatment leads to the downregulation of the MT1 receptor in lung adenocarcinoma cells, which is attributed to receptor endocytosis and lysosomal degradation via the canonical endo-lysosomal route. USP8 negatively regulates the endocytic degradation of the MT1 receptor incurred by melatonin exposure and thus protects lung adenocarcinoma cell growth. USP8 suppression by knockdown or pharmacological inhibition effectively deters cancer cell proliferation and sensitizes lung adenocarcinoma cells to melatonin in vitro. Furthermore, USP8 silencing significantly potentiates the anticancer effects of melatonin in xenograft tumor models.
Conclusion
The MT1 receptor responds to melatonin treatment and is endocytosed for lysosomal degradation that is counteracted by USP8. The inhibition of USP8 demonstrates tumor-suppressive effects and thus can be exploited as potential therapeutic strategy either as monotherapy or combined therapy with melatonin.
... ESCRT-0 facilitates initial capture of ubiquitylated receptors within specialised domains at the endosome [164]. STAM provides a common interaction site for two DUBs, USP8 and AMSH (also known as STAMBP), which are recruited to the endosome surface, via a complex set of interactions [165][166][167][168]. USP8 has variable effects upon receptor fate depending on its expression levels, but one key property dominates, which is its ability to stabilise components of the ESCRT complex, particularly ESCRT-0 [169]. ...
We now have a comprehensive inventory of ubiquitin system components. Understanding of any system also needs an appreciation of how components are organised together. Quantitative proteomics has provided us with a census of their relative populations in several model cell types. Here, by examining large scale unbiased data sets, we seek to identify and map those components, which principally reside on the major organelles of the endomembrane system. We present the consensus distribution of > 50 ubiquitin modifying enzymes, E2s, E3s and DUBs, that possess transmembrane domains. This analysis reveals that the ER and endosomal compartments have a diverse cast of resident E3s, whilst the Golgi and mitochondria operate with a more restricted palette. We describe key functions of ubiquitylation that are specific to each compartment and relate this to their signature complement of ubiquitin modifying components.
... Signal transducing adaptor molecule-binding protein (STAMBP) is an endosomeresident deubiquitinase in the Jab/MPN metalloenzyme (JAMM) family [114]. STAMBP regulates the endolysosomal cellular trafficking of ubiquitinated proteins such as NALP7 [115]. ...
In response to diverse pathogenic and danger signals, the cytosolic activation of the NLRP3 (NOD-, LRR-, and pyrin domain-containing (3)) inflammasome complex is a critical event in the maturation and release of some inflammatory cytokines in the state of an inflammatory response. After activation of the NLRP3 inflammasome, a series of cellular events occurs, including caspase 1-mediated proteolytic cleavage and maturation of the IL-1β and IL-18, followed by pyroptotic cell death. Therefore, the NLRP3 inflammasome has become a prime target for the resolution of many inflammatory disorders. Since NLRP3 inflammasome activation can be triggered by a wide range of stimuli and the activation process occurs in a complex, it is difficult to target the NLRP3 inflammasome. During the activation process, various post-translational modifications (PTM) of the NLRP3 protein are required to form a complex with other components. The regulation of ubiquitination and deubiquitination of NLRP3 has emerged as a potential therapeutic target for NLRP3 inflammasome-associated inflammatory disorders. In this review, we discuss the ubiquitination and deubiquitination system for NLRP3 inflammasome activation and the inhibitors that can be used as potential therapeutic agents to modulate the activation of the NLRP3 inflammasome.
... Monoubiquitination is associated with the endocytosis and lysosomal sorting of plasma membrane proteins, while the formation of lysine 48 (K48)-linked polyubiquitin chains is the primary signal targeting proteins to the 26S proteasome for degradation (35). To test the notion that PMAinduced reduction of Kv1.5 is through lysosomal degradation, the lysosomal inhibitor, bafilomycin A1 (Baf, 1 μM), or the proteasomal inhibitor MG132 (10 μM) was included during PMA (10 nM) treatment of Kv1.5-HEK cells for 3 h. ...
The voltage-gated potassium channel Kv1.5 plays important roles in the repolarization of atrial action potentials and regulation of the vascular tone. While the modulation of Kv1.5 function has been well studied, less is known about how the protein levels of Kv1.5 on the cell membrane are regulated. Here, through electrophysiological and biochemical analyses of Kv1.5 channels heterologously expressed in HEK293 cells and neonatal rat ventricular myocytes, as well as native Kv1.5 in human induced pluripotent stem cell (iPSC)-derived atrial cardiomyocytes, we found that activation of protein kinase C (PKC) with phorbol 12-myristate 13-acetate (PMA, 10 nM) diminished Kv1.5 current (IKv1.5) and protein levels of Kv1.5 in the plasma membrane. Mechanistically, PKC activation led to monoubiquitination and degradation of the mature Kv1.5 proteins. Overexpression of Vps24, a protein that sorts transmembrane proteins into lysosomes via the multivesicular body (MVB) pathway, accelerated whereas the lysosome inhibitor bafilomycin A1 completely prevented PKC-mediated Kv1.5 degradation. Kv1.5, but not Kv1.1, Kv1.2, Kv1.3 or Kv1.4, was uniquely sensitive to PMA treatment. Sequence alignments suggested that residues within the N-terminus of Kv1.5 are essential for PKC mediated Kv1.5 reduction. Using N-terminal truncation as well as site-directed mutagenesis, we identified that Thr15 is the target site for PKC that mediates endocytic degradation of Kv1.5 channels. These findings indicate that alteration of protein levels in the plasma membrane represents an important regulatory mechanism of Kv1.5 channel function under PKC activation conditions.
... Ubiquitination works as an engagement tool of the proteins with the endosomal sorting complexes required for transport (ESCRTs) (159). In fact, ubiquitination has been reported at several points along the endocytic pathway. ...
The GHR signaling pathway plays important roles in growth, metabolism, cell cycle control, immunity, homeostatic processes, and chemoresistance via both the JAK/STAT and the SRC pathways. Dysregulation of GHR signaling is associated with various diseases and chronic conditions such as acromegaly, cancer, aging, metabolic disease, fibroses, inflammation and autoimmunity. Numerous studies entailing the GHR signaling pathway have been conducted for various cancers. Diverse factors mediate the up- or down-regulation of GHR signaling through post-translational modifications. Of the numerous modifications, ubiquitination and deubiquitination are prominent events. Ubiquitination by E3 ligase attaches ubiquitins to target proteins and induces proteasomal degradation or starts the sequence of events that leads to endocytosis and lysosomal degradation. In this review, we discuss the role of first line effectors that act directly on the GHR at the cell surface including ADAM17, JAK2, SRC family member Lyn, Ubc13/CHIP, proteasome, βTrCP, CK2, STAT5b, and SOCS2. Activity of all, except JAK2, Lyn and STAT5b, counteract GHR signaling. Loss of their function increases the GH-induced signaling in favor of aging and certain chronic diseases, exemplified by increased lung cancer risk in case of a mutation in the SOCS2-GHR interaction site. Insight in their roles in GHR signaling can be applied for cancer and other therapeutic strategies.
... Ubiquitination is a common denominator in the targeting of substrates to the main protein degradation pathways (Clague and Urbé, 2010), including lysosomal degradation (reviewed in Clague and Urbé, 2006). Interestingly, we determined elevated proportions of ubiquitin-positive cortical interneurons evident in Dnmt1-deficient mice (50 ± 0.8%) compared to wild-type controls (39.5 ± 2%; * * P < 0.01, Student's t-test; n = 3 mice per genotype; Supplementary Figures S4e,f). ...
Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Dnmt1 deletion in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, conditional Dnmt1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is implicated in age- and disease-related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.
... The other complexes are sequentially recruited due to interaction sides for each other and membrane binding properties. AMSH, a K63-linked chain specific deubiquitinating enzyme, has been shown to bind to the SH3 domain of STAM and to promote recycling of the EGF receptor [155] [156] [157]. Thus at the stage of the early endosome the fate of a protein can still be changed from degradation to recycling. ...
From the discovery of ubiquitin and its function as signal for proteasomal degradation over 20 years ago to this days, it became evident that ubiquitin is a universal signal in eukaryotic cells. Ubiquitin in its different forms is involved in many versatile cellular processes. Knowing that the ubiquitin signal is differently translated, depending on its occurrences as mono-ubiquitin or poly-ubiquitin, raises the question: how do cells distinguish between the different occurrences of ubiquitin and translate it into the proper response? Proteins interacting with ubiquitin contain so called ubiquitin binding domains (UBDs), whereas the affinities to ubiquitin vary from a few _M to mM. So far only three (K63, K48 and linear chains) out of the eight possible chain-linkages can be produced in sufficient amounts to characterize their interaction with UBDs. K48- and K63- linked ubiquitin chains regulate different cellular events and need to be recognized by different proteins. Thus, it is of prime importance to characterize the binding of different UBDs to these two kinds of ubiquitin chains, as it can give important clues related to the general mechanism of chain discrimination by ubiquitin adapter proteins. Some isolated UBDs exhibit a preference for one chain linkage type over the other, whereas others do not discriminate between mono-ubiquitin or K63- and K48-linked chains. Interestingly, many ubiquitin adapter proteins harbor more than one UBD. STAM2 is a ubiquitin adapter protein, that is involved in endosomal receptor sorting and supposed to preferentially bind mono-ubiquitin and K63- over K48-linked ubiquitin. STAM2 contains two UBDs (a VHS and UIM domain) that were shown to bind to ubiquitin . The current manuscript shows that STAM2’s SH3 domain binds ubiquitin as well. To understand the function of the sequential arrangement of three UBDs in one protein, first binding of the individual VHS and UIM domains to monoubiquitin as well as K48- and K63-linked di-ubiquitin was investigated. This work shows, that the VHS domain displays a different mode of binding for K63- and K48-linked diubiquitin. In spite of the fact, that the apparent Kd for both chains is the same, only one VHS domain can bind to K48-linked di-ubiquitin chains (with a preference for the distal domain), whereas K63-linked di-ubiquitin can accommodate two VHS domains at a time. Since no conclusion can be drawn with respect to the apparent Kds, the different binding modes might gain more impact in consideration of the ensemble of three UBDs. Results presented in this manuscript, based on a construct containing the VHS and UIM domain, show that binding to K63- but not K48-linked di-ubiquitin is cooperative
... Through inhibiting USP2, ML364 potentiates the pro-degradation effects of HSP90 inhibitors toward ErbB2, which collectively elicit potent anti-cancer effects. either positive or negative regulation upon the endocytic degradation of cell surface proteins, primarily depending on locations of DUB action [44]. Receptor deubiquitylation occurring on early endosomes frequently promotes the recycling of receptors to the surface, while DUB on late endosomes/lysosomes retrieves ubiquitin molecules and facilitates lysosomal degradation of committed cargoes [25,27]. ...
ErbB2 overexpression identifies a subclass of breast cancer as ErbB2-positive that is frequently associated with poor prognosis. Current ErbB2-targeted therapies have profoundly improved patient outcomes, but mutations occurring in ErbB2 have been shown to confer drug resistance. Induction of ErbB2 degradation was proposed as an intriguing strategy to battle with ErbB2-positive breast cancer and reduced mutation-incurred drug resistance. Although multiple HSP90 inhibitors have been demonstrated to effectively trigger ErbB2 degradation, none succeeded in the clinical evaluations. To develop novel ErbB2-targeting strategies, we investigated the endocytic degradation and reversible ubiquitylation of ErbB2 in breast cancer. In this study, we reveal that HSP90 inhibition leads to efficient ubiquitylation and endocytic degradation of ErbB2 through the canonical endo-lysosomal route. USP2 associates with internalized ErbB2 and prevents its lysosomal sorting and degradation via exerting deubiquitylase activity. Accordingly, the USP2 inhibitor ML364 is capable of inducing ErbB2 ubiquitylation and accelerating its turnover. ML364 potentiates the pro-degradation effects of HSP90 inhibitors on ErbB2 and hence sensitizes ErbB2-positive breast cancer cells to HSP90 inhibition. The combination of USP2 and HSP90 inhibitors effectively restrains ErbB2-positive breast cancer xenograft growth in vivo. Based on these observations, we conclude that USP2 safeguards ErbB2 surface levels by antagonizing its ubiquitylation-mediated endocytic degradation, which can be exploited to design novel therapeutic strategies against ErbB2-driven malignancies as combinatorial treatment with HSP90 inhibitors.
... UBP1 was identified as a K13-interacting partner [41]. UBP1 is a member of a protein family that hydrolyses small C-terminal adducts of ubiquitin to generate the ubiquitin monomer, thereby increasing the available pool of ubiquitin [49,50]. Yeast Ubp1 has been proposed to promote endocytic recycling [51]. ...
Artemisinins – the frontline antimalarial drug class – are compromised by emerging resistance, putting at risk the lives of hundreds of thousands of people each year. Resistance is associated with mutations in a malaria parasite protein, called Kelch 13 (K13). Recent work suggests that K13 is located at the cytostome (cell mouth) that the parasite uses to take up hemoglobin. Here we explore the proposal that K13 mutations confer artemisinin resistance by dampening hemoglobin endocytosis. This model suggests that the resultant decrease in hemoglobin-derived heme reduces artemisinin activation, which is sufficient to enable parasite survival in the early ring stage of infection. A fuller understanding of the resistance mechanism will underpin efforts to develop alternative antimalarial strategies.
... Ubiquitination is a reversible reaction, with specific deubiquitinating enzymes (DUBs) that catalyze the removal of Ub-moieties for their recycling. DUBs serve to counterbalance ubiquitination reactions within the cell, thus dynamically contributing to the regulation of various cellular processes, such as endosomal sorting [11,[16][17][18]. ...
Ubiquitination regulates several biological processes, however the role of specific members of the ubiquitinome on intracellular membrane trafficking is not yet fully understood. Here, we search for ubiquitin-related genes implicated in protein membrane trafficking performing a High-Content siRNA Screening including 1187 genes of the human "ubiquitinome" using amyloid precursor protein (APP) as a reporter. We identified the deubiquitinating enzyme PSMD14, a subunit of the 19S regulatory particle of the proteasome, specific for K63-Ub chains in cells, as a novel regulator of Golgi-to-endoplasmic reticulum (ER) retrograde transport. Silencing or pharmacological inhibition of PSMD14 with Capzimin (CZM) caused a robust increase in APP levels at the Golgi apparatus and the swelling of this organelle. We showed that this phenotype is the result of rapid inhibition of Golgi-to-ER retrograde transport, a pathway implicated in the early steps of the autophagosomal formation. Indeed, we observed that inhibition of PSMD14 with CZM acts as a potent blocker of macroautophagy by a mechanism related to the retention of Atg9A and Rab1A at the Golgi apparatus. As pharmacological inhibition of the proteolytic core of the 20S proteasome did not recapitulate these effects, we concluded that PSMD14, and the K63-Ub chains, act as a crucial regulatory factor for macroautophagy by controlling Golgi-to-ER retrograde transport.
... The highly significant hits for Rab2A-GTP included STAMBPL1 and ARFGEF3. STAMBPL1 is a paralog of STAMBP (AMSH), an endosome-associated deubiquitinase that regulates entry of endocytosed proteins into the ESCRTdependent multi-vesicular body pathway (Clague and Urbé, 2006). Although STAMBPL1 has been shown to share with STAMBP a specificity for cleaving Lys63linked polyubiquitin chains, its function is unclear (Sato et al., 2008). ...
The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. The GTPases are precisely controlled by regulators that promote acquisition of GTP (GEFs) or its hydrolysis to GDP (GAPs). We report here MitoID, a method for identifying effectors and regulators by performing in vivo proximity biotinylation with mitochondrially-localized forms of the GTPases. Applying this to 11 human Rab GTPases identified many known effectors and GAPs, as well as putative novel effectors, with examples of the latter validated for Rab2, Rab5 and Rab9. MitoID can also efficiently identify effectors and GAPs of Rho and Ras family GTPases such as Cdc42, RhoA, Rheb, and N-Ras, and can identify GEFs by use of GDP-bound forms.
... In fact, these two Deubiquitinating (DUBs) enzymes are strongly associated to endosomes where they regulate the stability and ubiquitination status of ESCRT-0 members STAM and/or Hrs [30,[33][34][35][36][37][38][39] as well as of internalized receptors [27,28,30,[38][39][40][41]. Particularly, both AMSH and USP8/UBPY deubiquitinate the Epidermal Growth Factor Receptor (EGFR), a member of the receptor tyrosine kinase family (RTK), by acting at the level of the plasma membrane and/or of the endosome where deubiquitination of EGFR precedes its incorporation into MVBs [27,33,34,37,[41][42][43][44][45][46][47][48][49]. In addition to EGFR, USP8 deubiquitinates numerous plasma membrane receptors, making this enzyme a promising target in cancer therapy to overcome chemoresistance associated with RTK stabilization [50,51]. ...
Integration and down-regulation of cell growth and differentiation signals rely on plasma membrane receptors endocytosis and sorting towards either recycling vesicles or degradative lysosomes via multivesicular bodies (MVB). In this process, the endosomal sorting complex-III required for transport (ESCRT-III) controls membrane deformation and scission triggering intraluminal vesicle (ILV) formation at early endosomes. Here, we show that the ESCRT-III member CHMP1B can be ubiquitinated within a flexible loop known to undergo conformational changes during polymerization. We demonstrate further that CHMP1B is deubiquitinated by the ubiquitin specific protease USP8 (syn. UBPY) and found fully devoid of ubiquitin in a ~500 kDa large complex that also contains its known ESCRT-III partner IST1. Moreover, EGF stimulation induces the rapid and transient accumulation of ubiquitinated forms of CHMP1B on cell membranes. Accordingly, CHMP1B ubiquitination is necessary for CHMP1B function in both EGF receptor trafficking in human cells and wing development in Drosophila. From these observations, we propose that CHMP1B is dynamically regulated by ubiquitination in response to EGF and that USP8 triggers CHMP1B deubiquitination possibly favoring its subsequent assembly into a membrane-associated ESCRT-III polymer.
... Recent studies have screened DUBs involved in regulation of EGFR degradation including AMSH, USP8, USP9X, which regulated EGFR initial endocytosis by stabilization of Esp15 [38], and Cezanne-1, which was frequently amplified and promoting tumor aggressiveness in breast cancers [39], using siRNA library of the majority of human DUBs. Among them, Clague et al. has reported that AMSH and USP8 are required to interact with Hrs-STAM endosomal sorting complex at early endosome, regulating STAM stability [40,41]. However, Komada et al. showed that USP8 is recruited by Hrs-STAM and directly binds with ubiquitinated EGFR to deubiquitinate it [42]. ...
Previously we have reported that stratifin (SFN, 14-3-3 sigma) acts as a novel oncogene, accelerating the tumor initiation and progression of lung adenocarcinoma. Here, pull-down assay and LC-MS/MS analysis revealed that ubiquitin-specific protease 8 (USP8) specifically bound to SFN in lung adenocarcinoma cells. Both USP8 and SFN showed higher expression in human lung adenocarcinoma than in normal lung tissue, and USP8 expression was significantly correlated with SFN expression. Expression of SFN, but not of USP8, was associated with histological subtype, pathological stage, and poor prognosis. USP8 stabilizes receptor tyrosine kinases (RTKs) such as EGFR and MET by deubiquitination, contributing to the proliferative activity of many human cancers including non-small cell lung cancer. In vitro, USP8 binds to SFN and they co-localize at the early endosomes in lung adenocarcinoma cells. Moreover, USP8 or SFN knockdown leads to downregulation of tumor cellular proliferation and upregulation of apoptosis, p-EGFR or p-MET, which are related to the degradation pathway, and accumulation of ubiquitinated RTKs, leading to lysosomal degradation. Additionally, mutant USP8, which is unable to bind to SFN, reduces the expression of RTKs and p-STAT3. We also found that interaction with SFN is critical for USP8 to exert its autodeubiquitination function and avoid dephosphorylation by PP1. Our findings demonstrate that SFN enhances RTK stabilization through abnormal USP8 regulation in lung adenocarcinoma, suggesting that SFN could be a more suitable therapeutic target for lung adenocarcinoma than USP8.
... AMSH, another K 63 -selective DUB [118], participates in multivesicular body sorting [119]. The Rpn11(Poh1) subunit of 19S (PA700) regulator has deubiquitination function, with Zn 2+ dependent proteolysis [120][121] [122]. ...
... Both, UBPY and AMSH are implicated in the regulation of endosomal trafficking and interact with various members of the ESCRT-III family (Agromayor and Martin-Serrano 2006;McCullough et al. 2006;Kyuuma et al. 2007;Ma et al. 2007;Row et al. 2007;Solomons et al. 2011). Deubiquitination of internalized tyrosine kinase membrane receptors (RTKs) at the endosomal membranes precedes their incorporation into MVB vesicles and both AMSH and UBPY have been specifically implicated in the deubiquitination and the regulation of the RTK Epidermal Growth Factor Receptor (EGFR) (Agromayor and Martin-Serrano 2006;Bowers et al. 2006;Clague and Urbe 2006;Mizuno et al. 2006;Row et al. 2006;Alwan and van Leeuwen 2007;Ma et al. 2007;Ali et al. 2013;Savio et al. 2016). ...
I did my thesis in the group of Dr. Marie-Odile Fauvarque who implements strategies of molecular genetics on human cell culture models and in the Drosophila fly for the identification and study of the function of proteins in intracellular signaling. In this context, my work aimed to produce fundamental knowledge about the ubiquitin system in the control of the endocytic trafficking, in particular of membrane receptors involved in the inflammatory response (TNFR, ILR) or cell differentiation and growth (EGFR). I was particularly interested in the role of the complex formed by the interaction between an endocytic protein, CHMP1B, and the ubiquitin protease UBPY (synonym USP8). CHMP1B is a member of the ESCRT-III family that controls the biogenesis of intraluminal vesicles (ILVs) at the late endosomes to form multivesicular bodies (MVBs) Conformational change and polymerization at lipidic membrane processes are needed for CHMP1B function. MVBs fuse with the lysosomes, thus ensuring the proteolysis of the internalized receptors and the stoppage of the intracellular signaling. Alternatively, the receptors may be returned to the plasma membrane from early or late endosomes via recycling vesicles. Intracellular trafficking and receptor sorting in these different subcellular compartments play a major role in the activation, duration and termination of intracellular signals. The covalent bond of one or more ubiquitin (a highly conserved polypeptide of 76 amino acids) at the receptors is a major signal triggering their internalization. By hydrolyzing this ubiquitin, UBPY can stop the internalization of receptors at the plasma membrane, or promote their entry into the MVB. UBPY would thus play two opposing roles on the stability of the receptors depending on its level of action in the cell. The interaction between the two proteins CHMP1B and UBPY had been described in the literature in the two-hybrid system in yeast or by co-immunoprecipitation from cell lysates. However, the team's work showed no strong interaction between the domains of interaction of these two proteins in vitro and the function of this interaction in the endocytosis process had only been partially elucidated.During my thesis, I confirmed the existence of the CHMP1B-UBPY in cellulo complex, which is located mainly at the level of late endosomes. I determined the region involved in this interaction and proved that the existence of this complex makes possible the stabilization of both proteins into the cells. I then demonstrated the existence of monomeric and dimeric ubiquitinated forms of CHMP1B in which the binding of a molecule of ubiquitin to one of the two lysines of a flexible loop of the protein likely induces and/or stabilize a conformational conformation. In addition, UBPY hydrolyses this ubiquitin and promotes the accumulation of CHMP1B oligomers which are devoid of ubiquitin. Finally, the treatment of cells by EGF, which binds to EGFR and causes its internalization, induces transient recruitment of ubiquitinated CHMP1B dimers to the membranes. Analysis of the intracellular trafficking of EGFR and the morphogenesis of Drosophila wing in different genetic contexts has also shown that the ubiquitination of CHMP1B is essential to its function. My work has allowed me to formulate a completely new hypothesis in which the ubiquitination of CHMP1B induces an open conformation of the protein incapable of polymerizing in this state which is recruited in the form of dimers to the membrane of the endosomes and there the presence of UBPY induces the deubiquitination and the concomitant polymerization of CHMP1B, most probably in hetero-complexes with other members of the ESCRT-III family acting in concert for deformation and scission of the membranes.
Fms‐like tyrosine kinase‐3 (FLT3) is a commonly mutated gene in acute myeloid leukemia (AML). The two most common mutations are the internal‐tandem duplication domain (ITD) mutation and the tyrosine kinase domain (TKD) mutation. FLT3‐ITD and FLT3‐TKD exhibit distinct protein stability, cellular localization, and intracellular signaling. To understand the underlying mechanisms, we performed proximity labeling with TurboID to identify proteins that regulate FLT3‐ITD or ‐TKD differently. We found that BRCA1/BRCA2‐containing complex subunit 36 (BRCC36), a specific K63‐linked polyubiquitin deubiquitinase, was exclusively associated with ITD, not the wild type of FLT3 and TKD. Knockdown of BRCC36 resulted in decreased signal transducers and activators of transcription 5 phosphorylation and cell proliferation in ITD cells. Consistently, treatment with thiolutin, an inhibitor of BRCC36, specifically suppressed cell proliferation and induced cell apoptosis in ITD cells. Thiolutin efficiently affected leukemia cell lines expressing FLT3‐ITD cell viability and exhibited mutual synergies with quizartinib, a standard clinical medicine for AML. Furthermore, mutation of the lysine at 609 of ITD led to significant suppression of K63 polyubiquitination and decreased its stability, suggesting that K609 is a critical site for K63 ubiquitination specifically recognized by BRCC36. These data indicate that BRCC36 is a specific regulator for FLT3‐ITD, which may shed light on developing a novel therapeutic approach for AML.
The regulation of ubiquitylation is key for plant growth and development, in which the activities of ubiquitylating enzymes as well as deubiquitylating enzymes (DUBs) determine the stability or function of the modified proteins. In contrast with ubiquitylating enzymes, there are less numbers of DUBs. DUBs can be classified into seven protein families according to the amino acid sequence of their catalytic domains. The catalytic domains of animal and plant DUB families show high homology, whereas the regions outside of the catalytic site can vary a lot. By hydrolyzing the ubiquitin molecules from ubiquitylated proteins, DUBs control ubiquitin-dependent selective protein degradation pathways such as the proteasomal-, autophagic-, and endocytic degradation pathways. In the endocytic degradation pathway, DUBs can modulate the endocytic trafficking and thus the stability of plasma membrane proteins including receptors and transporters. To date, three DUB families were shown to control the endocytic degradation pathway namely associated molecule with the SH3 domain of STAM (AMSH) 3, ubiquitin-specific protease (UBP) 12 and UBP13, and ovarian tumor protease (OTU) 11 and OTU12. In this review we will summarize the activity, molecular functions, and target protein of these DUBs and how they contribute to the environmental response of plants.
Arteriovenous malformations (AVMs) are fast-flow vascular malformations and refer to important causes of intracerebral hemorrhage in young adults. Getting deep insight into the genetic pathogenesis of AVMs is necessary.
Herein, we identified two vital missense variants of G protein-coupled receptor (GPCR) associated sorting protein 1 (GPRASP1) in AVM patients for the first time and congruously determined to be loss-of-function (LoF) variants in endothelial cells. GPRASP1 LoF caused endothelial dysfunction in vitro and in vivo. Endothelial Gprasp1 knockout mice suffered a high probability of cerebral hemorrhage, AVMs, and exhibited vascular anomalies in multiple organs. GPR4 was identified to be an effective GPCR binding with GPRASP1 to develop endothelial disorders. GPRASP1 deletion activated GPR4/cAMP/MAPK signaling to disturb endothelial functions, thus contributing to vascular anomalies. Mechanistically, GPRASP1 promoted GPR4 degradation. GPRASP1 enabled GPR4 K63-linked ubiquitination, enhancing the binding of GPR4 and RABGEF1 to activate RAB5 for conversions from endocytic vesicles to endosomes, and subsequently increasing the interactions of GPR4 and ESCRT members to package GPR4 into multivesicular bodies or late endosomes for lysosome degradation. Notably, the GPR4 antagonist NE 52-QQ57 and JNK inhibitor SP600125 effectively rescued the vascular phenotype caused by endothelial Gprasp1 deletion. Our findings provided novel insights into the roles of GPRASP1 in AVMs and hinted at new therapeutic strategies.
PurposeThe epidermal growth factor receptor (EGFR) represents a top therapeutic target in the treatment of non-small cell lung cancer. EGFR expression is intricately modulated by receptor endocytosis, during which EGFR ubiquitylation and deubiquitylation play fundamental roles to govern receptor fate. This study aims to uncover novel aspects of the endocytic regulation of EGFR trafficking by deubiquitylases.Methods
The expression and ubiquitylation of EGFR in non-small cell lung cancer cells treated with deubiquitylase inhibitors were assessed by immunoblotting, immunoprecipitation and mass spectrometry analyses. The intracellular EGFR distribution was investigated using immunofluorescence and confocal microscopy assays, and colocalizations with endocytic compartments were examined using GFP-tagged Rab proteins as markers. The influence of the proteasomal deubiquitylase inhibitor b-AP15 on EGF- and HSP90 inhibitor-induced EGFR downregulation was evaluated by immunoblotting. The anticancer effects of b-AP15 were assessed by cell proliferation, colony formation and flow cytometry assays, as well as xenograft animal models.ResultsWe found that b-AP15 caused a dramatically enhanced ubiquitylation of EGFR in lung cancer cells. Treatment with b-AP15 decreased cell surface EGFR levels and accumulated EGFR on recycling endosomes marked with Rab4A and Rab11A. b-AP15 effectively repressed EGF- and HSP90 inhibitor-induced EGFR degradation. Lung cancer cells exposed to b-AP15 showed markedly reduced cell propagation and significantly increased cell apoptosis. Furthermore, b-AP15 effectively inhibited tumor xenograft growth in nude mice.Conclusion
Proteasomal USP14 and UCHL5 act collectively to promote cell surface recovery of EGFR. Inhibition of proteasomal deubiquitylase activity induces increased EGFR ubiquitylation and retention on recycling endosomes. The USP14 and UCHL5 dual inhibitor b-AP15 elicits potent tumor-suppressive effects to deter cell proliferation and induce apoptotic cell death in lung cancer.
Ubiquitin signaling is a conserved, widespread, and dynamic system in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization or stability. To regulate this system, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, post-translational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal–lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalanine residue of the flap interacts with a conserved aspartate residue of the Ins-1 β-turn to form a closed `lid' over the active site in the substrate-bound state. Analyses of these two residues (Phe403 and Asp315) in Sst2 showed that their interaction plays an important role in controlling the flexibility of Ins-2. The Lys63-linked diubiquitin substrate-bound form of Sst2 showed that the conserved phenylalanine also interacts with Thr316 of Ins-1, which is substituted by tyrosine in other AMSH orthologs. Although Thr316 makes no direct interaction with the substrate, its mutation to alanine resulted in a significant loss of activity. In order to understand the contribution of Thr316 to catalysis, the crystal structure of this mutant was determined. In spite of the effect of the mutation on catalytic activity, the structure of the Sst2 Thr316Ala mutant did not reveal significant changes in either the overall structure or the active-site arrangement relative to the wild type. The Phe403–Thr316 van der Waals interaction is impaired by the Thr316Ala mutation, abrogating the adoption of the closed active-site conformation required for catalysis. Since van der Waals interactions with phenylalanine are conserved across substrate-bound forms of AMSH-LP and Sst2, these interactions may be critical for loop immobilization and the positioning of the isopeptide bond of Lys63-linked polyubiquitin-chain substrates.
NFAT (Nuclear factor of activated T cells) transcription factors play important physiological roles in the development and function of many organs, notably in the immune system and nervous system. As a consequence, their dysregulation has been implicated in various human diseases such as cancer, neurodegenerative diseases, and auto-immune diseases. The regulation of NFAT activity by calcium-dependent nuclear-cytoplasmic shuttling has been extensively studied. In contrast, the regulation of NFAT protein level by the ubiquitin-proteasome system is still poorly understood. However, NFATs are short-lived proteins and regulation of their stability is critical for controlling their activity.In a previous study, my group has shown that the E3 ubiquitin-ligase Trim17 binds NFATc3 but does not promote its ubiquitination and rather stabilizes it. Preliminary results suggested that Trim39, a partner of Trim17, might be an E3 ubiquitin-ligase for NFATc3 and that SUMOylation of NFATc3 might modulate its stability. Therefore, the goal of my PhD was to understand the mechanisms through which Trim39, Trim17, and SUMO regulate the stability of NFATc3.During my PhD, I have characterized Trim39 as an E3 ubiquitin-ligase of NFATc3. Indeed, my results indicate that overexpression of Trim39, but not its inactive mutant, induces the ubiquitination of NFATc3 in cells. In contrast, silencing of endogenous Trim39 decreases the ubiquitination level of NFATc3. Recombinant Trim39 directly induces the ubiquitination of NFATc3 in vitro. Moreover, overexpression of Trim39 decreases the protein levels of NFATc3 whereas the silencing of Trim39 increases it. I have also shown that Trim17, which can bind Trim39, inhibits Trim39-mediated ubiquitination of NFATc3, both in cells and in vitro. Trim17 acts by both reducing the intrinsic E3 ubiquitin-ligase activity of Trim39 and by preventing the interaction between NFATc3 and Trim39. Furthermore, I found that a SUMOylation-deficient mutant of NFATc3 is less ubiquitinated and more stable than the wild type NFATc3, suggesting that SUMOylation of NFATc3 is important for its ubiquitination and degradation. Importantly, I identified one SUMO interacting motif (SIM) in the sequence of Trim39 through which Trim39 binds SUMO2 polymers via one of these SIMs. Mutation of this SIM in Trim39 or SUMOylation consensus sites in NFATc3 decreased the interaction between Trim39 and NFATc3, and the ubiquitination of NFATc3 mediated by Trim39. These results strongly suggest that Trim39 binds and ubiquitinates preferentially the SUMOylated forms of NFATc3 and therefore acts as a SUMO-targeted E3 ubiquitin-ligase (STUbL) for NFATc3. Finally, we have measured the impact of these mechanisms on the physiological function of NFATc3. I first found that Trim39 decreases the transcriptional activity of NFATc3. Furthermore, using primary cultures of cerebellar granule neurons as a model, we have shown that the mutation of the SUMOylation sites of NFATc3 and silencing of endogenous Trim39 enhances neuronal apoptosis, probably by stabilizing the NFATc3 protein. Taken together, these data indicate that Trim39 modulates neuronal apoptosis by acting as a STUbL for NFATc3 and by controlling its stability.
USP8 is a deubiquitinating enzyme in the family of ubiquitin-specific proteases (USPs) which can remove ubiquitin from the substrate and protect the substrate from degradation. The upregulated or mutated USP8 becomes hyperactivated and stabilizes numerous oncogenes or proto-oncogenes leading to cancer progression and survival by activating multiple signaling pathways. Moreover, USP8 inhibition is also important to overcome anticancer drug-resistant. This review is the first study to find, combine, analyze, and represent the multiple oncogenic signaling pathways with their downstream and upstream regulation activated or enhanced by USP8, which will help the researchers to find any therapeutic strategy for drug discovery by inhibiting or suppressing the multi-targeted USP8.
In non‐small cell lung cancer (NSCLC), activating mutations in the epidermal growth factor receptor (EGFR) induce sensitivity to EGFR tyrosine kinase inhibitors. Despite impressive clinical responses, patients ultimately relapse as a reservoir of drug‐tolerant cells ultimately leads to acquired resistance mechanisms. We performed an unbiased high‐throughput siRNA screen to identify proteins that abrogate the response of EGFR mutant NSCLC to EGFR targeted therapy. The deubiquitinase USP13 was a top hit resulting from this screen. Targeting USP13 increases the sensitivity to EGFR inhibition with small molecules in vitro and in vivo. USP13 selectively stabilizes mutant EGFR in a peptidase‐independent manner by counteracting the action of members of the Cbl family of E3 ubiquitin ligases. We conclude that USP13 is a strong mutant EGFR‐specific co‐target that could improve the treatment efficacy of EGFR targeted therapies.
The plasma membrane (PM), as border between the inside and the outside of a cell, is densely packed with proteins involved in the sensing and transmission of internal and external stimuli, as well as transport processes and is therefore vital for plant development as well as quick and accurate responses to the environment. It is consequently not surprising that several regulatory pathways participate in the tight regulation of the spatiotemporal control of PM proteins. Ubiquitination of PM proteins plays a key role in directing their entry into the endo-lysosomal system, serving as a signal for triggering endocytosis and further sorting for degradation. Nevertheless, a uniting picture of the different roles of the respective types of ubiquitination in the consecutive steps of down-regulation of membrane proteins is still missing. The trans-Golgi network (TGN), which acts as an early endosome (EE) in plants receives the endocytosed cargo, and here the decision is made to either recycled back to the PM or further delivered to the vacuole for degradation. A multi-complex machinery, the endosomal sorting complex required for transport (ESCRT), concentrates ubiquitinated proteins and ushers them into the intraluminal vesicles of multi-vesicular bodies (MVBs). Several ESCRTs have ubiquitin binding subunits, which anchor and guide the cargos through the endocytic degradation route. Basic enzymes and the mode of action in the early degradation steps of PM proteins are conserved in eukaryotes, yet many plant unique components exist, which are often essential in this pathway. Thus, deciphering the initial steps in the degradation of ubiquitinated PM proteins, which is the major focus of this review, will greatly contribute to the larger question of how plants mange to fine-tune their responses to their environment.
Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression, contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Deletion of Dnmt1 in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, DNMT1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is suggested to be essentially implicated in age- and disease- related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.
Ubiquitination regulates several biological processes. Here, we search for ubiquitin-related genes implicated in protein membrane trafficking performing a High-Content siRNA Screening including 1,187 genes of the human "ubiquitinome" using Amyloid Precursor Protein (APP) as a reporter. We identified the deubiquitinating enzyme PSMD14, a subunit of the 19S regulatory particle of the proteasome, specific for K63-Ub chains in cells, as a novel key regulator of Golgi-to-endoplasmic reticulum (ER) retrograde transport. Silencing or pharmacological inhibition of PSMD14 caused a robust and rapid inhibition of Golgi-to-ER retrograde transport which leads to a potent blockage of macroautophagy by a mechanism associated with the retention of Atg9A and Rab1A at the Golgi apparatus. Because pharmacological inhibition of the proteolytic core of the 20S proteasome did not recapitulate these effects, we concluded that PSMD14, and their K-63-Ub chains, act as a crucial regulator factor for macroautophagy by controlling Golgi-to-ER retrograde transport. Keywords: PSMD14, Ubiquitin, Retrograde, Trafficking, APP
Objectives:
Osteoarthritis (OA) is known to be a slowly progressive disease that alters all tissue compartments of the joint involved with a characteristic degradation of the cartilage, bone remodeling, and inflammation. One of the prominent symptoms in OA patients is pain, but a few radiological, inflammatory or structurally related biomarkers have shown little if any associations to pain. This study aimed to assess serum levels of 92 markers involved in inflammatory pathways in patients with knee OA (KOA) and evaluate their possible associations with the clinical pain intensity.
Methods:
Serum samples were collected from 127 knee KOA patients and 39 healthy participants with no knee pain. Each serum sample was analyzed for 92 inflammatory markers using the Proximity Extension Array (PEA) technology. Clinical pain intensity was assessed using a visual analog scale, and patients completed the Knee Injury and Osteoarthritis Outcome Score (KOOS) questionnaire.
Results:
Fifteen markers were significantly different when comparing KOA patient and healthy participants. Two markers, fibroblast growth factor-21 (FGF-21) and Eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1), correlated positively with pain intensity (R=0.235, P=0.008; R=0.233, P=0.008). Moreover, a linear regression model showed interleukin-6 (IL-6), macrophage colony-stimulating factor 1 (CSF-1), FGF-21 and tumor necrosis factor superfamily member 12 (TWEAK) as significant independent parameters for pain intensity.
Discussion:
The associations between specific cytokines and KOA pain intensities provide new insights into the understanding of the underlying factors driving the pain in OA.
BRCA1-BRCA2-containing complex subunit 3 (BRCC3), a Lys-63-specific deubiquitinase, is a member of the JAMM/MPN family of zinc metalloproteases. BRCC3 have been shown to promote the inflammasome activation by deubiquitinating NOD-like receptor containing pyrin domain 3 (NLRP3). We reported the involvement of neuronal inflammasome in Parkinson's Disease (PD), but the molecular mechanism remains unknown. In this study, we showed that BRCC3 expression was increased in PD models. Knock-down of BRCC3 with shRNA lentivirus decreased NLRP3 neuronal inflammasome. Interestingly, upregulating cyclin-dependent kinase 5 (Cdk5) increased the expression of BRCC3 in HEK293 cell, while inhibition of Cdk5 decreased the upregulated BRCC3 level in MPP+-induced PD cell model. The interaction between Cdk5 and BRCC3 was further confirmed by immunoprecipitation. Moreover, inhibition of Cdk5 suppressed the expression of NLRP3, pro-caspase-1, the adaptor molecule apoptosis-associated speck-like protein containing a CARD (ASC) and interleukin-1 beta (IL-1β). Besides, inhibition of BRCC3 blocked the increased secretion of IL-1β. Together, these results suggest that Cdk5-mediated BRCC3 expression may play a critical role in neuronal inflammation by regulating the NLRP3 inflammasome in PD.
Ligand binding to the cell surface receptors initiates signaling cascades that are commonly transduced through protein-protein interaction (PPI) network to activate a plethora of response pathways. However, tools to capture membrane PPI network are lacking. Here, we describe a cross-linking-aided mass spectrometry workflow for isolation and identification of signal-dependent EGFR proteome. We performed protein cross-linking in cell culture at various time points following EGF treatment followed by immunoprecipitation of endogenous EGFR and analysis of the associated proteins by quantitative mass spectrometry. We identified 140 proteins with high confidence during a 2h-time course by data-dependent acquisition and further validated the results by parallel reaction monitoring. A large proportion of proteins in the EGFR proteome function in endocytosis and intracellular protein transport. The EGFR proteome was highly dynamic with distinct temporal behavior; 10 proteins that appeared in all timepoints constitute the core proteome. Functional characterization showed that loss of the FYVE domain-containing proteins altered the EGFR intracellular distribution but had a minor effect on EGFR proteome or signaling. Thus, our results suggest that the EGFR proteome include functional regulators that influence EGFR signaling and bystanders that are captured as the components of endocytic vesicles. The high-resolution spatiotemporal information of these molecules facilitates the delineation of the many pathways that could determine the strength and duration of the signaling, as well as the location and the destination of the receptor.
The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. The GTPases are precisely controlled by regulators that promote acquisition of GTP (GEFs) or its hydrolysis to GDP (GAPs). We report here MitoID, a method for identifying effectors and regulators by performing in vivo proximity biotinylation with mitochondrially-localized forms of the GTPases. Applying this to 11 human Rab GTPases identified many known effectors and GAPs, as well as putative novel effectors, with examples of the latter validated for Rab2, Rab5, Rab9 and Rab11. MitoID can also efficiently identify effectors and GAPs of Rho and Ras family GTPases such as Cdc42, RhoA, Rheb, and N-Ras, and can identify GEFs by use of GDP-bound forms.
Objective(s)
The prognosis of osteoporosis is very poor, and it is very important to identify a biomarker for prevention of osteoporosis. In this study, we aimed to
identify candidate markers in osteoporosis and to investigate the role of candidate markers in osteogenic differentiation.
Materials and Methods
Using Weighted Gene Co-Expression Network analysis, we identified three hub genes might associate with osteoporosis. The mRNA expression of hub genes in osteoblasts from osteoporosis patients or healthy donor was detected by qRT-PCR. Using siRNA and overexpression, we investigated the role of hub gene BRCC3 in osteogenic differentiation by alkaline phosphatase staining and Alizarin red staining. Moreover, the role of β-catenin signaling in the osteogenic differentiation was detected by using β-catenin signaling inhibitor XAV939.
Results
We identified three hub genes that might associate with osteoporosis including BRCC3, UBE2N, and UBE2K. UBE2N mRNA and UBE2K mRNA were not changed in osteoblasts isolated from osteoporosis patients, compared with healthy donors, whereas BRCC3 mRNA was significantly increased. Depletion of BRCC3 promoted the activation of alkaline phosphatase and formation of calcified nodules in osteoblasts isolated from osteoporosis patients and up-regulated β-catenin expression. XAV939 reversed the BRCC3 siRNA-induced osteogenic differentiation. Additionally, inhibited osteogenic differentiation was also observed after BACC3 overexpression, and this was accompanied by decreased β-catenin expression.
Conclusion
BRCC3 is an important regulator for osteogenic differentiation of osteoblasts through β-catenin signaling, and it might be a promising target for osteoporosis treatment.
The deubiquitylating enzymes (DUBs, also known as deubiquitylases or deubiquitinases) maintain the dynamic state of the cellular ubiquitome by releasing conjugated ubiquitin from proteins. In light of the many cellular functions of ubiquitin, DUBs occupy key roles in almost all aspects of cell behaviour. Many DUBs show selectivity for particular ubiquitin linkage types or positions within ubiquitin chains. Others show chain-type promiscuity but can select a distinct palette of protein substrates via specific protein–protein interactions established through binding modules outside of the catalytic domain. The ubiquitin chain cleavage mode or chain linkage specificity has been related directly to biological functions. Examples include regulation of protein degradation and ubiquitin recycling by the proteasome, DNA repair pathways and innate immune signalling. DUB cleavage specificity is also being harnessed for analysis of ubiquitin chain architecture that is assembled on specific proteins. The recent development of highly specific DUB inhibitors heralds their emergence as a new class of therapeutic targets for numerous diseases.
La protéine CEP55 pour Centrosomal protein 55 kDa est un régulateur essentiel de la dernière étape de la division cellulaire appelée cytocinèse. En utilisant des approches de bioinformatique, structure-fonction et de biologie cellulaire, nous montrons que CEP55 comporte deux nouveaux domaines d'interaction à l'ubiquitine, qui sont similaires à ceux de la protéine NEMO, NOACEP55 et ZFCEP55 et qui régulent différemment la fonction de CEP55 durant la cytocinèse. Des études de modélisation structurale, mutagénèse dirigée et de biophysique de ces domaines ont permis de mettre en évidence que NOACEP55 adopte une structure dimérique de type " coiled-coil " et interagit préférentiellement avec des chaines d'ubiquitine linéaires (M1). Néanmoins, ZFCEP55 présente une architecture de type zinc finger ou UBZ et se lie préférentiellement avec des chaines d'ubiquitine K63 et M1. De plus, nous mettons en évidence que ZFCEP55 est indispensable au recrutement de CEP55 au midbody de façon dépendante de son interaction avec l'ubiquitine. A contrario, NOACEP55 joue un rôle déterminant en aval du recrutement de CEP55 au midbody. Dans un second volet, nous montrons que NOACEP55 et ZFCEP55 qui sont séparés par un domaine charnière riche en proline, interagissent in vitro de manière coopérative avec de longues chaines d'ubiquitine K63 et que cette interaction est modulée par phosphorylation et isomérisation d'acteurs physiologiques associés à CEP55. Enfin, ces résultats ont permis d'identifier par criblage de siRNA des ubiquitine ligases et déubiquitinases impliquées dans la cytocinèse, qui permettent de discuter du rôle de la signalisation de l'ubiquitine dans ce processus cellulaire.
In the mammalian brain, neuronal excitatory synaptic development, function, and plasticity largely rely on dynamic, activity-dependent changes in the macromolecular protein complex called the postsynaptic density (PSD). Activity-dependent Lys48-linked polyubiquitination and subsequent proteasomal degradation of key proteins in the PSD have been reported. However, investigations into the functions and regulatory mechanisms of Lys63-linked polyubiquitination, the second most abundant polyubiquitin form in synapses, have recently begun. Recent studies showed that a Lys63 linkage-specific deubiquitinase (DUB), cylindromatosis-associated DUB (CYLD) localizes to the PSD where its DUB activity is regulated by different kinases. In addition, Lys63-linked polyubiquitination of postsynaptic density 95 (PSD-95), a core scaffolding protein of the PSD, was identified and its functional significance in synaptic plasticity was characterized. In this review, we summarize these recent findings on Lys63-linked polyubiquitination in excitatory postsynapses, and also propose key questions and prospects about this emerging type of posttranslational modification of the PSD proteome.
The ubiquitin-dependent degradation of membrane proteins via the multivesicular body (MVB) pathway requires the Endosomal Sorting Complexes Required for Transport (ESCRT). This molecular machinery is composed of five distinct multi-subunit complexes. On the surface of endosomes, ESCRT-0, -I and -II bind to ubiquitinated membrane proteins, while ESCRT-III and Vps4 bud intraluminal vesicles (ILVs) into the lumen of the endosomes. By working together, ESCRTs package membrane proteins into ILVs and thereby generate MVBs. The fusion of mature MVBs with lysosomes delivers ILVs into the lysosomal lumen where the membrane proteins are degraded. Besides generating ILVs, the ESCRT machinery mediates for topologically related membrane budding processes at the plasma membrane and the nuclear envelop. In this chapter, we briefly discuss membrane protein ubiquitination, endocytosis, and summarize current knowledge on the ESCRT machinery in the MVB pathway.
We have followed the transfer of EGF-EGF receptor (EGFR) complexes from endosomal vacuoles that contain transferrin receptors (TfR) to lysosome vacuoles identified by their content of HRP loaded as a 15-min pulse 4 h previously. We show that the HRP-loaded lysosomes are lysosomal-associated membrane protein-1 (LAMP-1) positive, mannose-6-phosphate receptor (M6PR) negative. and contain active acid hydrolase. EGF-EGFR complexes are delivered to these lysosomes intact and are then rapidly degraded. Preactivating the HRP contained within the preloaded lysosomes inhibits the delivery of EGFR and degradation of EGF, and results in the accumulation of EGFR-containing multivesicular bodies (MVB). With time these accumulating MVB undergo a series of maturation changes that include the loss of TfR, the continued recruitment of EGFR, and the accumulation of internal vesicles, but they remain LAMP-1 and M6PR negative. The mature MVB are often seen to make direct contact with lysosomes containing preactivated HRP, but their perimeter membranes remain intact. Together our observations suggest that the transfer of EGF-EGFR complexes from the TfR-containing endosome compartment to the lysosomes that degrade them employs a single vacuolar intermediate, the maturing MVB, and can be achieved by a single heterotypic fusion step.
We have recently reported that the yeast plasma membrane uracil permease undergoes cell-surface ubiquitination, which is dependent on the Npi1/Rsp5 ubiquitin-protein ligase. Ubiquitination of this permease, like that of some other transporters and receptors, signals endocytosis of the protein, leading to its subsequent vacuolar degradation. This process does not involve the proteasome, which binds and degrades ubiquitin-protein conjugates carrying Lys48-linked ubiquitin chains. The data presented here show that ubiquitination and endocytosis of uracil permease are impaired in yeast cells lacking the Doa4p ubiquitin-isopeptidase. Both processes were rescued by overexpression of wild-type ubiquitin. Mutant ubiquitins carrying Lys-->Arg mutations at Lys29 and Lys48 restored normal permease ubiquitination. In contrast, a ubiquitin mutated at Lys63 did not restore permease polyubiquitination. Ubiquitin-permease conjugates are therefore extended through the Lys63 of ubiquitin. When polyubiquitination through Lys63 is blocked, the permease still undergoes endocytosis, but at a reduced rate. We have thus identified a natural target of Lys63-linked ubiquitin chains. We have also shown that monoubiquitination is sufficient to induce permease endocytosis, but that Lys63-linked ubiquitin chains appear to stimulate this process.
The ubiquitin pathway has been implicated in the regulation of the abundance of proteins that control cell growth and proliferation. We have identified and characterized a novel human ubiquitin isopeptidase, UBPY, which both as a recombinant protein and upon immunoprecipitation from cell extracts is able to cleave linear or isopeptide-linked ubiquitin chains. UBPY accumulates upon growth stimulation of starved human fibroblasts, and its levels decrease in response to growth arrest induced by cell-cell contact. Inhibition of UBPY accumulation by antisense plasmid microinjection prevents fibroblasts from entering S-phase in response to serum stimulation. By increasing or decreasing the cellular abundance of UBPY or by overexpressing a catalytic site mutant, we detect substantial changes in the total pattern of protein ubiquitination, which correlate stringently with cell proliferation. Our results suggest that UBPY plays a role in regulating the overall function of the ubiquitin-proteasome pathway. Affecting the function of a specific UBP in vivo could provide novel tools for controlling mammalian cell proliferation.
We molecularly cloned a new Grb2 family member, named Grf40, containing the common SH3-SH2-SH3 motif. Expression of Grf40 is predominant in hematopoietic cells, particularly T cells. Grf40 binds to the SH2 domain-containing leukocyte protein of 76 kD (SLP-76) via its SH3 domain more tightly than Grb2. Incidentally, Grf40 binds to linker for activation of T cells (LAT) possibly via its SH2 domain. Overexpression of wild-type Grf40 in Jurkat cells induced a significant increase of SLP-76-dependent interleukin (IL)-2 promoter and nuclear factor of activated T cell (NF-AT) activation upon T cell receptor (TCR) stimulation, whereas the COOH-terminal SH3-deleted Grf40 mutant lacked any recognizable increase in IL-2 promoter activity. Furthermore, the SH2-deleted Grf40 mutant led to a marked inhibition of these regulatory activities, the effect of which is apparently stronger than that of the SH2-deleted Grb2 mutant. Our data suggest that Grf40 is an adaptor molecule involved in TCR-mediated signaling through a more efficient interaction than Grb2 with SLP-76 and LAT.
STAM containing an SH3 (Src homology 3) domain and an immunoreceptor tyrosine-based activation motif was previously revealed
to be implicated in signaling pathways immediately downstream of Jak2 and Jak3 tyrosine kinases associated with cytokine receptors.
We molecularly cloned a novel molecule interacting with the SH3 domain of STAM, which was named AMSH (associatedmolecule with the SH3 domain of STAM). AMSH contains a putative bipartite nuclear localization signal and a homologous region of a c-Jun activation
domain-binding protein 1 (JAB1) subdomain in addition to a binding site for the SH3 domain of STAM. AMSH mutant deleted of
the C-terminal half conferred dominant negative effects on signaling for DNA synthesis and c-myc induction mediated by interleukin 2 and granulocyte macrophage-colony-stimulating factor. These results suggest that AMSH
plays a critical role in the cytokine-mediated intracellular signal transduction downstream of the Jak2/Jak3·STAM complex.
Hrs-binding protein (Hbp) is a Src homology 3 (SH3) domain-containing protein that tightly associates with Hrs. Hbp together
with Hrs is thought to play a regulatory role in endocytic trafficking of growth factor-receptor complexes through early endosomes.
Association of Hbp with a binding partner(s) via the SH3 domain seems to be essential for Hbp to exert its function. In this
study, we searched for Hbp-binding proteins by a far Western screening and isolated a mouse cDNA clone encoding a deubiquitinating
enzyme mUBPY as an Hbp SH3-binding protein. mUBPY has two Hbp-SH3 domain binding sites. Mutagenic analysis identified a consensus
sequence PX(V/I)(D/N)RXXKP as the Hbp-SH3 domain binding motif. It is a novel SH3-binding motif and does not contain the canonical proline-rich consensus
binding motif, PXXP. Ubiquitination of growth factor receptors is thought to regulate their intracellular degradation. Thus, UBPY may play a
regulatory role in the degradation by interaction with the SH3 domain of Hbp via the novel SH3-binding motif.
Previous experiments suggested that trafficking of the a-factor transporter Ste6 of Saccharomyces cerevisiae to the yeast vacuole is regulated by ubiquitination. To define the ubiquitination-dependent step in the trafficking pathway, we examined the intracellular localization of Ste6 in the ubiquitination-deficient doa4 mutant by immunofluorescence experiments, with a Ste6-green fluorescent protein fusion protein and by sucrose density gradient fractionation. We found that Ste6 accumulated at the vacuolar membrane in the doa4 mutant and not at the cell surface. Experiments with a doa4 pep4 double mutant showed that Ste6 uptake into the lumen of the vacuole is inhibited in the doa4 mutant. The uptake defect could be suppressed by expression of additional ubiquitin, indicating that it is primarily the result of a lowered ubiquitin level (and thus of reduced ubiquitination) and not the result of a deubiquitination defect. Based on our findings, we propose that ubiquitination of Ste6 or of a trafficking factor is required for Ste6 sorting into the multivesicular bodies pathway. In addition, we obtained evidence suggesting that Ste6 recycles between an internal compartment and the plasma membrane.
Inhibitory Smads, i.e. Smad6 and Smad7, are potent antagonists of the BMP-Smad pathway by interacting with activated bone morphogenetic protein (BMP) type I receptors and thereby preventing the activation of receptor-regulated Smads, or by competing with activated R-Smads for heteromeric complex formation with Smad4. The molecular mechanisms that underlie the regulation of I-Smad activity have remained elusive. Here we report the identification of a cytoplasmic protein, previously termed associated molecule with the SH3 domain of STAM (AMSH), as a direct binding partner for Smad6. AMSH interacts with Smad6, but not with R- and Co-Smads, upon BMP receptor activation in cultured cells. Consistent with this finding, stimulation of cells with BMP induces a co-localization of Smad6 with AMSH in the cytoplasm. Ectopic expression of AMSH prolongs BMP-induced Smad1 phosphorylation, and potentiates BMP-induced activation of transcriptional reporter activity, growth arrest and apoptosis. The data strongly suggest that the molecular mechanism by which AMSH exerts its action is by inhibiting the binding of Smad6 to activated type I receptors or activated R-Smads.
We used yeast “two-hybrid” screening to isolate cDNA-encoding proteins interacting with the N-terminal domain of the Ras nucleotide
exchange factor CDC25Mm. Three independent overlapping clones were isolated from a mouse embryo cDNA library. The full-length cDNA was cloned by
RACE-polymerase chain reaction. It encodes a large protein (1080 amino acids) highly homologous to the human deubiquitinating
enzyme hUBPy and contains a well conserved domain typical of ubiquitin isopeptidases. Therefore we called this new protein
mouse UBPy (mUBPy). Northern blot analysis revealed a 4-kilobase mRNA present in several mouse tissues and highly expressed
in testis; a good level of expression was also found in brain, where CDC25Mm is exclusively expressed. Using a glutathione S-transferase fusion protein, we demonstrated an “in vitro” interaction between mUBPy and the N-terminal half (amino acids 1–625) of CDC25Mm. In addition “in vivo” interaction was demonstrated after cotransfection in mammalian cells. We also showed that CDC25Mm, expressed in HEK293 cells, is ubiquitinated and that the coexpression of mUBPy decreases its ubiquitination. In addition
the half-life of CDC25Mm protein was considerably increased in the presence of mUBPy. The specific function of the human homolog
hUBPy is not defined, although its expression was correlated with cell proliferation. Our results suggest that mUBPy may play
a role in controlling degradation of CDC25Mm, thus regulating the level of this Ras-guanine nucleotide exchange factor.
The hepatocyte growth factor-regulated tyrosine kinase substrate, Hrs, has been implicated in intracellular trafficking and signal transduction. Hrs contains a phosphatidylinositol 3-phosphate-binding FYVE domain that contributes to its endosomal targeting. Here we show that Hrs and EEA1, a FYVE domain protein involved in endocytic membrane fusion, are localized to different regions of early endosomes. We demonstrate that Hrs co-localizes with clathrin, and that the C-terminus of Hrs contains a functional clathrin box motif that interacts directly with the terminal beta-propeller domain of clathrin heavy chain. A massive recruitment of clathrin to early endosomes was observed in cells transfected with Hrs, but not with Hrs lacking the C-terminus. Furthermore, the phosphatidylinositol 3-kinase inhibitor wortmannin caused the dissociation of both Hrs and clathrin from endosomes. While overexpression of Hrs did not affect endocytosis and recycling of transferrin, endocytosed epidermal growth factor and dextran were retained in early endosomes. These results provide a molecular mechanism for the recruitment of clathrin onto early endosomes and suggest a function for Hrs in trafficking from early to late endosomes.
Yeast endosomes, like those in animal cells, invaginate their membranes to form internal vesicles. The resulting multivesicular bodies fuse with the vacuole, the lysosome equivalent, delivering the internal vesicles for degradation. We have partially purified internal vesicles and analysed their content. Besides the known component carboxypeptidase S (Cps1p), we identified a polyphosphatase (Phm5p), a presumptive haem oxygenase (Ylr205p/Hmx1p) and a protein of unknown function (Yjl151p/Sna3p). All are membrane proteins, and appear to be cargo molecules rather than part of the vesicle-forming machinery. We show that both Phm5p and Cps1p are ubiquitylated, and that in a doa4 mutant, which has reduced levels of free ubiquitin, Cps1p, Phm5p and Hmx1p are mis-sorted to the vacuolar membrane. Mutation of Lys 6 in the cytoplasmic tail of Phm5p disrupts its sorting, but sorting is restored, even in doa4 cells, by the biosynthetic addition of a single ubiquitin chain. In contrast, Sna3p enters internal vesicles in a ubiquitin-independent manner. Thus, ubiquitin acts as a signal for the partitioning of some, but not all, membrane proteins into invaginating endosomal vesicles.
AMSH, a molecule that associates with STAM1, is involved in the in vitro cell growth signaling mediated by interleukin 2 and
granulocyte-macrophage colony-stimulating factor. To investigate the in vivo functional role of AMSH, we have generated AMSH-deficient
mice by gene targeting. The AMSH-deficient mice were morphologically indistinguishable from their littermates at birth, and
histopathological examinations revealed normal morphogenesis in all tissues tested. However, all the AMSH-deficient mice exhibited
postnatal growth retardation and died between postnatal day 19 (P19) and P23. Examination of brain sections at P6 demonstrated
significant loss of neurons and apoptotic cells in the CA1 subfield of the hippocampus. Brain atrophy developed by P16 and
was accompanied by complete loss of the CA1 neurons in the hippocampus and marked atrophy of the cerebral cortex. Furthermore,
AMSH-deficient hippocampal neuronal cells were unable to survive in vitro, even in the presence of several stimulatory cytokines,
while AMSH-deficient cerebellar neurons, thymocytes, and embryonic fibroblasts survived normally. Taken together, these observations
indicate that AMSH is an essential molecule for the survival of neuronal cells in early postnatal mice.
Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes.
Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically
relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display
ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated
a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions
among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1),
a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions,
many of which were confirmed in vivo by coimmunoprecipitation.
In many cells endosomal vacuoles show clathrin coats of which the function is unknown. Herein, we show that this coat is predominantly present on early endosomes and has a characteristic bilayered appearance in the electron microscope. By immunoelectron microscopy we show that the coat contains clathrin heavy as well as light chain, but lacks the adaptor complexes AP1, AP2, and AP3, by which it differs from clathrin coats on endocytic vesicles and recycling endosomes. The coat is insensitive to short incubations with brefeldin A, but disappears in the presence of the phosphatidylinositol 3-kinase inhibitor wortmannin. No association of endosomal coated areas with tracks of tubulin or actin was found. By quantitative immunoelectron microscopy, we found that the lysosomal-targeted receptors for growth hormone (GHR) and epidermal growth factor are concentrated in the coated membrane areas, whereas the recycling transferrin receptor is not. In addition, we found that the proteasomal inhibitor MG 132 induces a redistribution of a truncated GHR (GHR-369) toward recycling vesicles, which coincided with a redistribution of endosomal vacuole-associated GHR-369 to the noncoated areas of the limiting membrane. Together, these data suggest a role for the bilayered clathrin coat on vacuolar endosomes in targeting of proteins to lysosomes.
After endocytosis, some membrane proteins recycle from early endosomes to the plasma membrane whereas others are transported to late endosomes and lysosomes for degradation. Conjugation with the small polypeptide ubiquitin is a signal for lysosomal sorting. Here we show that the hepatocyte growth factor-regulated tyrosine kinase substrate, Hrs, is involved in the endosomal sorting of ubiquitinated membrane proteins. Hrs contains a clathrin-binding domain, and by electron microscopy we show that Hrs localizes to flat clathrin lattices on early endosomes. We demonstrate that Hrs binds directly to ubiquitin by way of a ubiquitin-interacting motif (UIM), and that ubiquitinated proteins localize specifically to Hrs- and clathrin-containing microdomains. Whereas endocytosed transferrin receptors fail to colocalize with Hrs and rapidly recycle to the cell surface, transferrin receptors that are fused to ubiquitin interact with Hrs, localize to Hrs- and clathrin-containing microdomains and are sorted to the degradative pathway. Overexpression of Hrs strongly and specifically inhibits recycling of ubiquitinated transferrin receptors by a mechanism that requires a functional UIM. We conclude that Hrs sorts ubiquitinated membrane proteins into clathrin-coated microdomains of early endosomes, thereby preventing their recycling to the cell surface.
The 26S proteasome mediates degradation of ubiquitin-conjugated proteins. Although ubiquitin is recycled from proteasome substrates,
the molecular basis of deubiquitination at the proteasome and its relation to substrate degradation remain unknown. The Rpn11
subunit of the proteasome lid subcomplex contains a highly conserved Jab1/MPN domain–associated metalloisopeptidase (JAMM)
motif—EXnHXHX10D. Mutation of the predicted active-site histidines to alanine (rpn11AXA) was lethal and stabilized ubiquitin pathway substrates in yeast. Rpn11AXA mutant proteasomes assembled normally but failed to either deubiquitinate or degrade ubiquitinated Sic1 in vitro. Our findings
reveal an unexpected coupling between substrate deubiquitination and degradation and suggest a unifying rationale for the
presence of the lid in eukaryotic proteasomes.
Three macromolecular assemblages, the lid complex of the proteasome, the COP9-Signalosome (CSN) and the eIF3 complex, all consist of multiple proteins harboring MPN and PCI domains. Up to now, no specific function for any of these proteins has been defined, nor has the importance of these motifs been elucidated. In particular Rpn11, a lid subunit, serves as the paradigm for MPN-containing proteins as it is highly conserved and important for proteasome function.
We have identified a sequence motif, termed the MPN+ motif, which is highly conserved in a subset of MPN domain proteins such as Rpn11 and Csn5/Jab1, but is not present outside of this subfamily. The MPN+ motif consists of five polar residues that resemble the active site residues of hydrolytic enzyme classes, particularly that of metalloproteases. By using site-directed mutagenesis, we show that the MPN+ residues are important for the function of Rpn11, while a highly conserved Cys residue outside of the MPN+ motif is not essential. Single amino acid substitutions in MPN+ residues all show similar phenotypes, including slow growth, sensitivity to temperature and amino acid analogs, and general proteasome-dependent proteolysis defects.
The MPN+ motif is abundant in certain MPN-domain proteins, including newly identified proteins of eukaryotes, bacteria and archaea thought to act outside of the traditional large PCI/MPN complexes. The putative catalytic nature of the MPN+ motif makes it a good candidate for a pivotal enzymatic function, possibly a proteasome-associated deubiquitinating activity and a CSN-associated Nedd8/Rub1-removing activity.
STAM1 and STAM2, which have been identified as regulators of receptor signaling and trafficking, interact directly with Hrs,
which mediates the endocytic sorting of ubiquitinated membrane proteins. The STAM proteins interact with the same coiled-coil
domain that is involved in the targeting of Hrs to endosomes. In this work, we show that STAM1 and STAM2, as well as an endocytic
regulator protein, Eps15, can be co-immunoprecipitated with Hrs both from membrane and cytosolic fractions and that recombinant
Hrs, STAM1/STAM2, and Eps15 form a ternary complex. We find that overexpression of Hrs causes a strong recruitment of STAM2
to endosome membranes. Moreover, STAM2, like Hrs and Eps15, binds ubiquitin, and Hrs, STAM2, and Eps15 colocalize with ubiquitinated
proteins in clathrin-containing endosomal microdomains. The localization of Hrs, STAM2, Eps15, and clathrin to endosome membranes
is controlled by the AAA ATPase mVps4, which has been implicated in multivesicular body formation. Depletion of cellular Hrs
by small interfering RNA results in a strongly reduced recruitment of STAM2 to endosome membranes and an impaired degradation
of endocytosed epidermal growth factor receptors. We propose that Hrs, Eps15, and STAM proteins function in a multivalent
complex that sorts ubiquitinated proteins into the multivesicular body pathway.
Many cellular proteins are post-translationally modified by the addition of a single ubiquitin or a polyubiquitin chain. Among these are receptor tyrosine kinases (RTKs), which undergo ligand-dependent ubiquitination. The ubiquitination of RTKs has become recognized as an important signal for their endocytosis and degradation in the lysosome; however, it is not clear whether ubiquitination itself is sufficient for this process or simply participates in its regulation. The issue is further complicated by the fact that RTKs are thought to be polyubiquitinated - a modification that is linked to protein degradation by the proteasome. By contrast, monoubiquitination has been associated with diverse proteasome-independent cellular functions including intracellular protein movement. Here we show that the epidermal growth factor and platelet-derived growth factor receptors are not polyubiquitinated but rather are monoubiquitinated at multiple sites after their ligand-induced activation. By using different biochemical and molecular genetics approaches, we show that a single ubiquitin is sufficient for both receptor internalization and degradation. Thus, monoubiquitination is the principal signal responsible for the movement of RTKs from the plasma membrane to the lysosome.
Growth factors stimulate specific receptor tyrosine kinases, but subsequent receptor endocytosis terminates signaling. The ubiquitin ligase c-Cbl targets epidermal growth factor receptors (EGFRs) to endocytosis by tagging them with multiple ubiquitin molecules. However, the type of ubiquitylation is unknown; whereas polyubiquitin chains signal proteasomal degradation, ubiquitin monomers control other processes. We report that in isolation c-Cbl mediates monoubiquitylation rather than polyubiquitylation of EGFRs. Consistent with the sufficiency of monoubiquitylation, when fused to the tail of EGFR, a single ubiquitin induces receptor endocytosis and degradation in cells. By using receptor and ubiquitin mutants, we infer that c-Cbl attaches a founder monoubiquitin to the kinase domain of EGFR and this is complemented by the conjugation of additional monoubiquitins. Hence, receptor tyrosine kinases are desensitized through conjugation of multiple monoubiquitins, which is distinct from polyubiquitin-dependent proteasomal degradation.
Although some exceptional motifs have been identified, it is well known that the PXXP motif is the motif of ligand proteins generally recognized by the Src homology 3 (SH3) domain. SH3-ligand interactions are
usually weak, with ordinary KD ∼ 10 μm. The structural basis for a tight and specific association (KD = 0.24 μm) between Gads SH3 and a novel motif, PX(V/I)(D/N)RXXKP, was revealed in a previous structural analysis of the complex formed between them. In this paper, we report the crystal
structure of the signal transducing adaptor molecule-2 (STAM2) SH3 domain in complex with a peptide with a novel motif derived
from a ligand protein, UBPY. The derived KD value for this complex is 27 μm. The notable difference in affinity for these parallel complexes may be explained because the STAM2 SH3 structure does not
provide a specificity pocket for binding, whereas the Gads SH3 structure does. Instead, the structure of STAM2 SH3 is analogous
to that of Grb2 SH3 which, in addition to normal PXXP ligands, has also been shown to moderately recognize the novel motif discussed herein. Thus, the extremely tight interaction
observed between Gads SH3 and the novel motif is caused not by an innate ability of the novel motif but rather by an evolutionary
change in the Gads SH3 domain. Instead, SH3 domains of STAM2 and Grb2 retain the moderate characteristics of recognizing their
ligand proteins like other SH3 domains for appropriate transient interactions between signaling molecules.
Transforming growth factor-betas (TGF-betas), bone morphogenetic proteins (BMPs) and activins are important regulators of developmental cell growth and differentiation. Signaling by these factors is mediated chiefly by the Smad family of latent transcription factors.
There are a large number of uncharacterized cDNA clones that code for novel proteins with homology to known signaling molecules. We have identified a novel molecule from the HUGE database that is related to a previously known molecule, AMSH (associated molecule with the SH3 domain of STAM), an adapter shown to be involved in BMP signaling. Both of these molecules contain a coiled-coil domain located within the amino-terminus region and a JAB (Domain in Jun kinase activation domain binding protein and proteasomal subunits) domain at the carboxy-terminus. We show that this novel molecule, which we have designated AMSH-2, is widely expressed and its overexpression potentiates activation of TGF-beta-dependent promoters. Coimmunoprecipitation studies indicated that Smad7 and Smad2, but not Smad3 or 4, interact with AMSH-2. We show that overexpression of AMSH-2 decreases the inhibitory effect of Smad7 on TGF-beta signaling. Finally, we demonstrate that knocking down AMSH-2 expression by RNA interference decreases the activation of 3TP-lux reporter in response to TGF-beta.
This report implicates AMSH and AMSH-2 as a novel family of molecules that positively regulate the TGF-beta signaling pathway. Our results suggest that this effect could be partially explained by AMSH-2 mediated decrease of the action of Smad7 on TGF-beta signaling pathway.
RING-finger proteins play crucial roles in ubiquitination events involved in diverse cellular processes including signal transduction, differentiation and apoptosis. Most of the RING-finger proteins have E3-ubiquitin ligase activity. RNF11 is a small RING-finger protein and harbors a RING-H2 domain and a PY motif that could facilitate protein:protein interaction(s) involved in oncogenesis. To isolate RNF11 protein partners and determine its role in normal and cancer cells, we performed yeast two-hybrid screening. Among 18 in-frame positive clones, three were found to be ZBRK1, Eps15 and AMSH (associated molecule with the SH3 domain of STAM). ZBRK1 is a KRAB domain containing Zinc-finger protein and is known to repress target gene transcription in a BRCA1-dependent manner. Eps15 is monoubiquitinated and is part of an essential complex involved in the endocytosis of plasma membrane receptors via the clathrin-mediated internalization pathway. Recent studies have shown that AMSH protein is involved in BMP/TGF-beta signaling pathway by binding to Smad6 and Smad7. The association of RNF11 with these binding partners suggests that it would be involved in biological processes such as gene transcription, BMP/TGF-beta signaling and ubiquitination-associated events. Previously, we have shown that RNF11 interacts with the HECT-type E3 ligases AIP4 and Smurf2. Here, we show that RNF11 binds to AMSH in mammalian cells and that this interaction is independent of the RNF11 RING-finger domain and the PY motif. Our results also demonstrate that AMSH is ubiquitinated by Smurf2 E3 ligase in the presence of RNF11 and that a consequent reduction in its steady-state level requires both RNF11 and Smurf2. RNF11 therefore recruits AMSH to Smurf2 for ubiquitination, leading to its degradation by the 26S proteasome. The potential functions of RNF11-mediated degradation of AMSH in breast cancer are discussed.
Nrdp1 is a RING finger-containing E3 ubiquitin ligase that physically interacts with and regulates steady-state cellular levels
of the ErbB3 and ErbB4 receptor tyrosine kinases and has been implicated in the degradation of the inhibitor-of-apoptosis
protein BRUCE. Here we demonstrate that the Nrdp1 protein undergoes efficient proteasome-dependent degradation and that mutations
in its RING finger domain that disrupt ubiquitin ligase activity enhance stability. These observations suggest that Nrdp1
self-ubiquitination and stability could play an important role in regulating the activity of this protein. Using affinity
chromatography, we identified the deubiquitinating enzyme USP8 (also called Ubpy) as a protein that physically interacts with
Nrdp1. Nrdp1 and USP8 could be coimmunoprecipitated, and in transfected cells USP8 specifically bound to Nrdp1 but not cbl,
a RING finger E3 ligase involved in ligand-stimulated epidermal growth factor receptor down-regulation. The USP8 rhodanese
and catalytic domains mediated Nrdp1 binding. USP8 markedly enhanced the stability of Nrdp1, and a point mutant that disrupts
USP8 catalytic activity destabilized endogenous Nrdp1. Our results indicate that Nrdp1 is a specific target for the USP8 deubiquitinating
enzyme and are consistent with a model where USP8 augments Nrdp1 activity by mediating its stabilization.
The JAMM (JAB1/MPN/Mov34 metalloenzyme) motif has been proposed to provide the active site for isopeptidase activity associated with the Rpn11/POH1 subunit of the 19S-proteasome and the Csn5-subunit of the signalosome. We have looked for similar activity in associated molecule with the SH3 domain of STAM (AMSH), a JAMM domain-containing protein that associates with the SH3-domain of STAM, a protein, which regulates receptor sorting at the endosome. We demonstrate isopeptidase activity against K48-linked tetraubiquitin and K63-linked polyubiquitin chains to generate di-ubiquitin and free ubiquitin, respectively. An inactivating mutation (D348A) in AMSH leads to accumulation of ubiquitin on endosomes and the concomitant stabilization of a ubiquitinated form of STAM, which requires an intact ubiquitin interaction motif (UIM) within STAM. Short interfering RNA knockdown of AMSH enhances the degradation rate of EGF receptor (EGFR) following acute stimulation and ubiquitinated EGFR provides a substrate for AMSH in vitro. We propose that AMSH is a deubiquitinating enzyme with functions at the endosome, which oppose the ubiquitin-dependent sorting of receptors to lysosomes.
Ubiquitination directs the sorting of cell surface receptors and other integral membrane proteins into the multivesicular body (MVB) pathway. Cargo proteins are subsequently deubiquitinated before their enclosure within MVB vesicles. In Saccharomyces cerevisiae, Bro1 functions at a late step of MVB sorting and is required for cargo protein deubiquitination. We show that the loss of Bro1 function is suppressed by the overexpression of DOA4, which encodes the ubiquitin thiolesterase required for the removal of ubiquitin from MVB cargoes. Overexpression of DOA4 restores cargo protein deubiquitination and sorting via the MVB pathway and reverses the abnormal endosomal morphology typical of bro1 mutant cells, resulting in the restoration of multivesicular endosomes. We further demonstrate that Doa4 interacts with Bro1 on endosomal membranes and that the recruitment of Doa4 to endosomes requires Bro1. Thus, our results point to a key role for Bro1 in coordinating the timing and location of deubiquitination by Doa4 in the MVB pathway.
Acute stimulation of the receptor for the hepatocyte growth factor/scatter factor Met leads to receptor monoubiquitination and down-regulation through the lysosomal degradation pathway. We have determined that the Met receptor undergoes multiple monoubiquitination as opposed to the appendage of polyubiquitin chains. Nevertheless, overexpression of ubiquitin in HEK293T cells enhances the rate of Met receptor degradation, in contrast to a point mutant of ubiquitin (K48R) that cannot form Lys(48)-linked polyubiquitin chains. Furthermore, an enhancement of Met degradation is also seen under conditions where the proteasome is inhibited by lactacystin. We propose that this reflects polyubiquitin-dependent sorting of Met, as the overexpression of ubiquitin but not K48R ubiquitin also restores hepatocyte growth factor-dependent phosphorylation of the endosomal coat protein Hrs from inhibition by lactacystin. Our data indicate a requirement for K48R-linked polyubiquitin for Met endosomal trafficking independent of its canonical function of targeting for proteasomal degradation.
Deubiquitinating enzymes (Dubs) are potential regulators of ubiquitination-dependent processes. Here, we focus on a member of the yeast ubiquitin-specific processing protease (Ubp) family, the Ubp1 protein. We could show that Ubp1 exists in two forms: a longer membrane-anchored form (mUbp1) and a shorter soluble form (sUbp1) that seem to be independently expressed from the same gene. The membrane-associated mUbp1 variant could be localized to the endoplasmic reticulum (ER) membrane by sucrose density gradient centrifugation and by immunofluorescence microscopy. Overexpression of the soluble Ubp1 variant stabilizes the ATP-binding cassette-transporter Ste6, which is transported to the lysosome-like vacuole for degradation, and whose transport is regulated by ubiquitination. Ste6 stabilization was not the result of a general increase in deubiquitination activity, because overexpression of Ubp1 had no effect on the degradation of the ER-associated degradation substrate carboxypeptidase Y* and most importantly on Ste6 ubiquitination itself. Also, overexpression of another yeast Dub, Ubp3, had no effect on Ste6 turnover. This suggests that the Ubp1 target is a component of the protein transport machinery. On Ubp1 overexpression, Ste6 accumulates at the cell surface, which is consistent with a role of Ubp1 at the internalization step of endocytosis or with enhanced recycling to the cell surface from an internal compartment.
Sorting of signal-transducing cell surface receptors within multivesicular bodies (MVBs) is required for their rapid down-regulation and degradation within lysosomes. Yeast mutants defective in late stages of transport to the vacuole/lysosome accumulate MVBs. We demonstrate that the membrane glycoprotein carboxypeptidase S and the G protein-coupled receptor Ste2p are targeted into the vacuole lumen, and this process requires a subset of VPS gene products essential for normal endosome function. The PtdIns(3)P 5-kinase activity of Fab1p, which converts the product of the Vps34p PtdIns 3-kinase PtdIns(3)P into PtdIns(3,5)P2, also is required for cargo-selective sorting into the vacuole lumen. These findings demonstrate a role for phosphoinositide signaling at distinct stages of vacuolar/lysosomal protein transport and couple PtdIns(3,5)P2 synthesis to regulation of MVB sorting.
e Saccharomyces cerevisiae Doa4 deubiquitinating enzyme is required for the rapid degradation of protein substrates of the ubiquitin-proteasome pathway. Previous work suggested that Doa4 functions late in the pathway, possibly by deubiquitinating (poly)-ubiquitin-substrate intermediates associated with the 26S proteasome. We now provide evidence for physical and functional interaction between Doa4 and the proteasome. Genetic interaction is indicated by the mutual enhancement of defects associated with a deletion of DOA4 or a proteasome mutation when the two mutations are combined. Physical association of Doa4 and the proteasome was investigated with a new yeast 26S proteasome purification procedure, by which we find that a sizeable fraction of Doa4 copurifies with the protease. Another yeast deubiquitinating enzyme, Ubp5, which is related in sequence to Doa4 but cannot substitute for it even when overproduced, does not associate with the proteasome. DOA4-UBP5 chimeras were made by a novel PCR/yeast recombination method and used to identify an N-terminal 310-residue domain of Doa4 that, when appended to the catalytic domain of Ubp5, conferred Doa4 function, consistent with Ubp enzymes having a modular architecture. Unlike Ubp5, a functional Doa4-Ubp5 chimera associates with the proteasome, suggesting that proteasome binding is important for Doa4 function. Together, these data support a model in which Doa4 promotes proteolysis through removal of ubiquitin from proteolytic intermediates on the proteasome before or after initiation of substrate breakdown.
Attachment of ubiquitin to cellular proteins frequently targets them to the 26S proteasome for degradation. In addition, ubiquitination of cell surface proteins stimulates their endocytosis and eventual degradation in the vacuole or lysosome. In the yeast Saccharomyces cerevisiae, ubiquitin is a long-lived protein, so it must be efficiently recycled from the proteolytic intermediates to which it becomes linked. We identified previously a yeast deubiquitinating enzyme, Doa4, that plays a central role in ubiquitin-dependent proteolysis by the proteasome. Biochemical and genetic data suggest that Doa4 action is closely linked to that of the proteasome. Here we provide evidence that Doa4 is required for recycling ubiquitin from ubiquitinated substrates targeted to the proteasome and, surprisingly, to the vacuole as well. In the doa4Delta mutant, ubiquitin is strongly depleted under certain conditions, most notably as cells approach stationary phase. Ubiquitin depletion precedes a striking loss of cell viability in stationary phase doa4Delta cells. This loss of viability and several other defects of doa4Delta cells are rescued by provision of additional ubiquitin. Ubiquitin becomes depleted in the mutant because it is degraded much more rapidly than in wild-type cells. Aberrant ubiquitin degradation can be partially suppressed by mutation of the proteasome or by inactivation of vacuolar proteolysis or endocytosis. We propose that Doa4 helps recycle ubiquitin from both proteasome-bound ubiquitinated intermediates and membrane proteins destined for destruction in the vacuole.
The Saccharomyces cerevisiae DOA4 gene encodes a deubiquitinating enzyme that is required for rapid degradation of ubiquitin-proteasome pathway substrates. Both genetic and biochemical data suggest that Doa4 acts in this pathway by facilitating ubiquitin recycling from ubiquitinated intermediates targeted to the proteasome. Here we describe the isolation of 12 spontaneous extragenic suppressors of the doa4-1 mutation; these involve seven different genes, six of which were cloned. Surprisingly, all of the cloned DID (Doa4-independent degradation) genes encode components of the vacuolar protein-sorting (Vps) pathway. In particular, all are class E Vps factors, which function in the maturation of a late endosome/prevacuolar compartment into multivesicular bodies that then fuse with the vacuole. Four of the six Did proteins are structurally related, suggesting an overlap in function. In wild-type and several vps strains, Doa4-green fluorescent protein displays a cytoplasmic/nuclear distribution. However, in cells lacking the Vps4/Did6 ATPase, a large fraction of Doa4-green fluorescent protein, like several other Vps factors, concentrates at the late endosome-like class E compartment adjacent to the vacuole. These results suggest an unanticipated connection between protein deubiquitination and endomembrane protein trafficking in which Doa4 acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins en route to the vacuole.
Responses to extracellular stimuli are often transduced from cell-surface
receptors to protein tyrosine kinases which, when activated, initiate the
formation of protein complexes that transmit signals throughout the cell.
A prominent component of these complexes is the product of the proto-oncogene
c-Cbl, which specifically targets activated protein tyrosine kinases
and regulates their signalling. How, then, does this multidomain protein shape
the responses generated by these signalling complexes?
The intimate relationship between receptor trafficking and signalling is beginning to reveal its secrets. Receptor endocytosis provides a mechanism for attenuation of signalling by transfer of receptors to degradative compartments. However, it can also determine signalling output by providing a different combination of downstream effectors at endocytic compartments compared with the plasma membrane. Rab5, Hrs and Cbl, are three examples of proteins that can influence both tyrosine kinase receptor trafficking and signalling pathways. By operating at this intersection, they are well placed to couple these aspects of cell function. Each element of the Rab5 GTPase cycle is influenced by signal transduction events, which will correspondingly influence recruitment of effector proteins and receptor distribution. Hrs and Cbl, which both undergo tyrosine phosphorylation in response to growth factor stimulation, are believed to influence receptor sorting in the early endosome and engage in multiple interactions, which may play a direct role in signalling cascades.
Like other enveloped viruses, HIV-1 uses cellular machinery to bud from infected cells. We now show that Tsg101 protein, which functions in vacuolar protein sorting (Vps), is required for HIV-1 budding. The UEV domain of Tsg101 binds to an essential tetrapeptide (PTAP) motif within the p6 domain of the structural Gag protein and also to ubiquitin. Depletion of cellular Tsg101 by small interfering RNA arrests HIV-1 budding at a late stage, and budding is rescued by reintroduction of Tsg101. Dominant negative mutant Vps4 proteins that inhibit vacuolar protein sorting also arrest HIV-1 and MLV budding. These observations suggest that retroviruses bud by appropriating cellular machinery normally used in the Vps pathway to form multivesicular bodies.
Membrane proteins that are degraded in the vacuole of Saccharomyces cerevisiae are sorted into discrete intralumenal vesicles, analogous to the internal membranes of multi-vesiculated bodies (MVBs). Recently, it has shown that the attachment of ubiquitin (Ub) mediates sorting into lumenal membranes. We describe a complex of Vps27p and Hse1p that localizes to endosomal compartments and is required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. The Vps27p-Hse1p complex binds to Ub and requires multiple Ub Interaction Motifs (UIMs). Mutation of these motifs results in specific defects in the sorting of ubiquitinated proteins into the vacuolar lumen. However, the recycling of Golgi proteins and the generation of lumenal membranes proceeds normally in Delta UIM mutants. These data support a model in which the Vps27p-Hse1p complex has multiple functions at the endosome, one of which is as a sorting receptor for ubiquitinated membrane proteins destined for degradation.
Lysosomally directed receptors are concentrated at a 'bilayered' clathrin coat on the face of sorting endosomes. This coat is highly enriched in Hrs protein, which can potentially serve as an adaptor between ubiquitinated receptors and clathrin.
The 26S proteasome is responsible for most intracellular proteolysis in eukaryotes. Efficient substrate recognition relies on conjugation of substrates with multiple ubiquitin molecules and recognition of the polyubiquitin moiety by the 19S regulatory complex--a multisubunit assembly that is bound to either end of the cylindrical 20S proteasome core. Only unfolded proteins can pass through narrow axial channels into the central proteolytic chamber of the 20S core, so the attached polyubiquitin chain must be released to allow full translocation of the substrate polypeptide. Whereas unfolding is rate-limiting for the degradation of some substrates and appears to involve chaperone-like activities associated with the proteasome, the importance and mechanism of degradation-associated deubiquitination has remained unclear. Here we report that the POH1 (also known as Rpn11 in yeast) subunit of the 19S complex is responsible for substrate deubiquitination during proteasomal degradation. The inability to remove ubiquitin can be rate-limiting for degradation in vitro and is lethal to yeast. Unlike all other known deubiquitinating enzymes (DUBs) that are cysteine proteases, POH1 appears to be a Zn(2+)-dependent protease.
Ubiquitylation is emerging as a versatile device for controlling cellular functions. Here, we propose that monoubiquitylation is rapidly induced by signalling events and allows the establishment of protein-protein interactions between monoubiquitylated proteins and partners that contain distinct ubiquitin-binding domains. We also put forward speculative models for the regulation of monoubiquitylation versus polyubiquitylation.
We have isolated a cDNA clone encoding a new AMSH (associated molecule with the SH3 domain of STAM) family protein, termed AMSH-like protein (AMSH-LP). AMSH-LP has similar characteristics to AMSH; both AMSH-LP and AMSH are expressed ubiquitously in various human tissues, contain a putative nuclear localization signal (NLS), an Mpr/Pad1/N-terminal (MPN) domain, and a Jab1/MPN domain metalloenzyme (JAMM) motif in their structures, and are excluded from the nucleus when lacking either the NLS or MPN domain. Moreover, we observed an enhancement of interleukin 2 (IL-2)-mediated c-myc induction in AMSH-LP-transfected cells similar to that seen in AMSH-transfected cells, suggesting a functional similarity between AMSH-LP and AMSH. However, the present study demonstrated that AMSH-LP, unlike AMSH, fails to bind to the SH3 domains of STAM1 (signal transducing adaptor molecule 1) and Grb2. These results suggest that AMSH-LP and AMSH may have different functions.
Associated Molecule with SH3 domain of STAM (AMSH) plays a critical role in the cytokine-mediated intracellular signal transduction downstream of the Jak2/Jak3-STAM complex. We newly identified a family molecule of AMSH, AMSH-FP (AMSH-Family Protein) in the mouse brain. AMSH-FP encodes the intracellular protein and has a highly conserved JAB1 Subdomain Homologous (JSH) region, suggesting that AMSH-FP may act as adaptor of gene transcription and/or regulation system. AMSH-FP has two splicing forms, one is expressed in various tissues, whereas the other one is restricted to expression in testis. We named the abundant type AMSH-FPalpha and the testis type AMSH-FPbeta. AMSH-FPbeta is a variant lacking N-terminal 166 amino acid residues of AMSH-FPalpha. Analysis of the 5(')-untranslated regions in AMSH-FPalpha and AMSH-FPbeta mRNAs and exon-intron structure of AMSH-FP gene suggests that testis-specific transcripts are generated due to alternative promoter usage and/or alternative splicing. Importantly, AMSH-FPbeta mRNA was not detected in juvenile and infertile mouse testis but was restrictively expressed in the haploid stage of testicular germ cells in the normal mature testis. We suggested that AMSH-FPbeta had a functional role in the spermiogenesis.
The ste12+ gene of Schizosaccharomyces pombe codes for a phosphatidylinositol (PI) 3-phosphate 5'-kinase, which is required for efficient mating. Suppressor mutants for sterility of ste12Delta cells were screened for. Most of the mutant genes turned out to be recessive. Six genes were cloned and the open reading frames responsible for the suppressor activity were identified. They included genes coding for proteins with domains homologous to calcium transporters, casein kinase II, UBC13, AMSH, Vps23p, and Vps27p of Saccharomyces cerevisiae. Disruption of these genes resulted in suppression of the defects of the ste12Delta cells, including low mating efficiency and formation of large vacuoles. Since many of these gene products are homologous to the proteins involved in vesicle transport, sterility caused by inactivation of ste12 may be due to a disordered vesicle transport system.
Hepatocyte growth factor regulated tyrosine kinase substrate (Hrs), a main component of the 'bilayered' clathrin coat on sorting endosomes, was originally identified as a substrate of activated tyrosine kinase receptors. We have analysed Hrs phosphorylation in response to epidermal growth factor (EGF) stimulation and show that the evolutionary conserved tyrosines Y329 and Y334 provide the principal phosphorylation sites. Hrs is proposed to concentrate ubiquitinated receptors within clathrin-coated regions via direct interaction with its UIM (ubiquitin interaction motif) domain. We show that the same UIM domain is necessary for EGF-stimulated tyrosine phosphorylation of Hrs. Over-expression of wild-type Hrs or a double mutant, Y329/334F, defective in EGF-dependent phosphorylation, both substantially retard EGF receptor (EGFR) degradation by inhibiting internal vesicle formation and thereby preventing EGFR incorporation into lumenal vesicles of the multivesicular bodies. In contrast, mutation or deletion of the Hrs-UIM domain strongly suppresses this effect. In addition the UIM-deletion and point mutants are also observed on internal membranes, indicating a failure to dissociate from the endosomal membrane prior to incorporation of the receptor complex into lumenal vesicles. Our data suggest a role for the UIM-domain of Hrs in actively retaining EGFR at the limiting membrane of endosomes as a prelude to lumenal vesicle formation.
Conjugation with ubiquitin acts as a sorting signal for proteins in the endocytic and biosynthetic pathways at the endosome. Signal-transducing adaptor molecule (STAM) proteins, STAM1 and STAM2, are associated with hepatocyte growth factor-regulated substrate (Hrs) but their function remains unknown. Herein, we show that STAM proteins bind ubiquitin and ubiquitinated proteins and that the tandemly located VHS (Vps27/Hrs/STAM) domain and ubiquitin-interacting motif serve as the binding site(s). STAM proteins colocalize with Hrs on the early endosome. Overexpression of STAM proteins, but not their mutants lacking the ubiquitin-binding activity, causes the accumulation of ubiquitinated proteins and ligand-activated epidermal growth factor receptor on the early endosome. These results suggest that through interaction with ubiquitinated cargo proteins on the early endosome via the VHS domain and ubiquitin-interacting motif, STAM proteins participate in the sorting of cargo proteins for trafficking to the lysosome.
The STAM family proteins, STAM1 and STAM2/EAST/Hbp, are phosphotyrosine proteins that contain SH3 domains and ubiquitin-interacting motifs. Their yeast homologue, Hse1, and its binding protein, Vps27, are involved in the vacuolar membrane transport machinery. Here we show that STAM1 and STAM2 are localized to the endosomal membrane. Some of these complexes contain Eps15, an endocytic protein, which accumulates in clumps upon expression of a dominant-negative form of Vps4-A, an AAA-type ATPase, that is required for normal endosome function. These results support the idea that the STAMs are mammalian vacuolar protein sorting (Vps) proteins. We also demonstrate that ligand-mediated epidermal growth factor receptor (EGFR) degradation is partially but not completely impaired in both Hrs(-/-) and STAM1(-/-)STAM2(-/-) mouse embryonic fibroblasts. Furthermore, endosome swelling is seen in both Hrs(-/-) and STAM1(-/-)STAM2(-/-) cells. These results suggest that the STAMs and Hrs play important roles in the mammalian endosomal/vacuolar protein sorting pathway.
HIV release requires TSG101, a cellular factor that sorts proteins into vesicles that bud into multivesicular bodies (MVB). To test whether other proteins involved in MVB biogenesis (the class E proteins) also participate in HIV release, we identified 22 candidate human class E proteins. These proteins were connected into a coherent network by 43 different protein-protein interactions, with AIP1 playing a key role in linking complexes that act early (TSG101/ESCRT-I) and late (CHMP4/ESCRT-III) in the pathway. AIP1 also binds the HIV-1 p6(Gag) and EIAV p9(Gag) proteins, indicating that it can function directly in virus budding. Human class E proteins were found in HIV-1 particles, and dominant-negative mutants of late-acting human class E proteins arrested HIV-1 budding through plasmal and endosomal membranes. These studies define a protein network required for human MVB biogenesis and indicate that the entire network participates in the release of HIV and probably many other viruses.
The endosomal protein Hrs plays a central role in the downregulation of receptors. A set of recent studies reveals a link between Hrs and the multiprotein complex ESCRT (endosome-associated complex required for transport) machinery that promotes inward vesiculation at the limiting membrane of the sorting endosome. A conserved sequence motif, PT/(S)AP, found in structural proteins of several RNA viruses (e.g. HIV Gag) promotes release of virus from the cell by recruiting the ESCRT machinery to the viral budding sites at the plasma membrane. The same motif is also found in Hrs and recruits the ESCRT I complex to endosomes through direct interaction with one of its components called TSG101. Fusion of Hrs with the gag gene of HIV-1 lacking this motif can complement a defect in virus budding. Further challenging data indicate a wider role for Hrs in the regulation of endosome dynamics.
The active ubiquitin E3 ligase GRAIL is crucial in the induction of CD4 T cell anergy. Here we show that GRAIL is associated with and regulated by two isoforms of the ubiquitin-specific protease otubain 1. In lethally irradiated mice reconstituted with bone marrow cells from T cell receptor-transgenic mice retrovirally transduced to express the genes encoding these proteases, otubain 1-expressing cells contained negligible amounts of endogenous GRAIL, proliferated well and produced large amounts of interleukin 2 after antigenic stimulation. In contrast, cells expressing the alternatively spliced isoform, otubain 1 alternative reading frame 1, contained large amounts of endogenous GRAIL and were functionally anergic, and they proliferated poorly and produced undetectable interleukin 2 when stimulated in a similar way. Thus, these two proteins have opposing epistatic functions in controlling the stability of GRAIL expression and the resultant anergy phenotype in T cells.
Ten class E Vps proteins in yeast are known components of the ESCRT complexes I, II and III, which are required for the sorting of proteins to the lumenal membranes of multivesicular bodies. We used the yeast 2 hybrid system to analyze the protein-protein interactions of all 17 soluble class E Vps proteins, as well as proteins thought to be required for the ubiquitination and deubiquitination of cargo proteins at multivesicular bodies. We identified novel interactions between yeast ESCRT complex components suggesting that ESCRTI binds to both ESCRTII and ESCRTIII. These interactions were confirmed by GST pull-down experiments. Our data indicate that the link between ESCRTI and ESCRTIII is via Vps28p and Vps37p/Srn2p binding directly to Vps20p, as well as through indirect interactions via ESCRTII. This is in contrast to the situation in mammalian cells where ESCRTI and ESCRTIII interact indirectly via ALIX, the mammalian homologue of yeast proteins Vps31p/Bro1p and Rim20p. Our data also enable us to link all soluble class E Vps proteins to the ESCRT complexes. We propose the formation of a large multimeric complex on the endosome membrane consisting of ESCRTI, ESCRTII, ESCRTIII and other associated proteins.
Ubiquitin is the founding member of a family of structurally conserved proteins that regulate a host of processes in eukaryotic cells. Ubiquitin and its relatives carry out their functions through covalent attachment to other cellular proteins, thereby changing the stability, localization, or activity of the target protein. This article reviews the basic biochemistry of these protein conjugation reactions, focusing on ubiquitin itself and emphasizing recent insights into mechanism and specificity.