Restoration of cellular ubiquitin reverses impairments in neuronal development caused by disruption of the polyubiquitin gene Ubb

Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development

Ubiquitination involves three types of enzymes (E1, E2, and E3) that sequentially attach ubiquitin (Ub) to target proteins. This posttranslational modification controls key cellular processes, such as the degradation, endocytosis, subcellular localization and activity of proteins. Ubiquitination, which can be reversed by deubiquitinating enzymes (DUBs), plays important roles during brain development. Furthermore, deregulation of the Ub system is linked to the pathogenesis of various diseases, including neurodegenerative disorders. We used a publicly available RNA-seq database to perform an extensive genome-wide gene expression analysis of the core components of the ubiquitination machinery, covering Ub genes as well as E1, E2, E3 and DUB genes. The ubiquitination network was governed by only Uba1 and Ube2m, the predominant E1 and E2 genes, respectively; their expression was positively regulated during cortical formation. The principal genes encoding HECT (homologous to the E6-AP carboxyl terminus), RBR (RING-in-between-RING), and RING (really interesting new gene) E3 Ub ligases were also highly regulated. Pja1, Dtx3 (RING ligases) and Stub1 (U-box RING) were the most highly expressed E3 Ub ligase genes and displayed distinct developmental expression patterns. Moreover, more than 80 DUB genes were expressed during corticogenesis, with two prominent genes, Uch-l1 and Usp22, showing highly upregulated expression. Several components of the Ub system overexpressed in cancers were also highly expressed in the cerebral cortex under conditions not related to tumour formation or progression. Altogether, this work provides an in-depth overview of transcriptomic changes during embryonic formation of the cerebral cortex. The data also offer new insight into the characterization of the Ub system and may contribute to a better understanding of its involvement in the pathogenesis of neurodevelopmental disorders.

SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development

Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3^−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3^−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.

The Ubiquitinated Axon: Local Control of Axon Development and Function by Ubiquitin

Ubiquitin tagging sets protein fate. With a wide range of possible patterns and reversibility, ubiquitination can assume many shapes to meet specific demands of a particular cell across time and space. In neurons, unique cells with functionally distinct axons and dendrites harboring dynamic synapses, the ubiquitin code is exploited at the height of its power. Indeed, wide expression of ubiquitination and proteasome machinery at synapses, a diverse brain ubiquitome, and the existence of ubiquitin-related neurodevelopmental diseases support a fundamental role of ubiquitin signaling in the developing and mature brain. While special attention has been given to dendritic ubiquitin-dependent control, how axonal biology is governed by this small but versatile molecule has been considerably less discussed. Herein, we set out to explore the ubiquitin-mediated spatiotemporal control of an axon's lifetime: from its differentiation and growth through presynaptic formation, function, and pruning.

The Dose-Dependent Pleiotropic Effects of the UBB+1 Ubiquitin Mutant

The proteolytic machinery activity diminishes with age, leading to abnormal accumulation of aberrant proteins; furthermore, a decline in protein degradation capacity is associated with multiple age-related proteinopathies. Cellular proteostasis can be maintained via the removal of ubiquitin (Ub)-tagged damaged and redundant proteins by the ubiquitin-proteasome system (UPS). However, during aging, central nervous system (CNS) cells begin to express a frameshift-mutated Ub, UBB⁺¹. Its accumulation is a neuropathological hallmark of tauopathy, including Alzheimer’s disease and polyglutamine diseases. Mechanistically, in cell-free and cell-based systems, an increase in the UBB⁺¹ concentration disrupts proteasome processivity, leading to increased aggregation of toxic proteins. On the other hand, a low level of UBB⁺¹ improves stress resistance and extends lifespan. Here we summarize recent findings regarding the impact of UBB⁺¹ on Ub signaling and neurodegeneration. We also review the molecular basis of how UBB⁺¹ affects UPS components as well as its dose-dependent switch between cytoprotective and cytotoxic roles.

Ubiquitin Homeostasis Is Disrupted in TDP-43 and FUS Cell Models of ALS

A major feature of amyotrophic lateral sclerosis (ALS) pathology is the accumulation of ubiquitin (Ub) into intracellular inclusions. This sequestration of Ub may reduce the availability of free Ub, disrupting Ub homeostasis and ultimately compromising cellular function and survival. We previously reported significant disturbance of Ub homeostasis in neuronal-like cells expressing mutant SOD1. Here, we show that Ub homeostasis is also perturbed in neuronal-like cells expressing either TDP-43 or FUS. The expression of mutant TDP-43 and mutant FUS led to UPS dysfunction, which was associated with a redistribution of Ub and depletion of the free Ub pool. Redistribution of Ub is also a feature of sporadic ALS, with an increase in Ub signal associated with inclusions and no compensatory increase in Ub expression. Together, these findings suggest that alterations to Ub homeostasis caused by the misfolding and aggregation of ALS-associated proteins play an important role in the pathogenesis of ALS.

Disruption of the polyubiquitin gene Ubb reduces the self-renewal capacity of neural stem cells

Ubiquitin (Ub) is a highly conserved eukaryotic protein that plays pivotal roles in cellular signal transduction, differentiation, and proteolysis. Although we have previously reported that disruption of the polyubiquitin gene Ubb is associated with the dysregulated differentiation of neural stem cells (NSCs) into neurons, it is unclear how gene expression patterns are altered in Ubb knockout (KO) NSCs, and whether this altered gene expression contributes to Ubb KO neural phenotypes. To answer these questions, we used RNA-Seq to compare the transcriptomes of Ubb KO NSCs and Ubb heterozygous (HT) controls. We found that the expression levels of most proliferation markers were decreased in Ubb KO NSCs. To determine whether the reduced levels of proliferation markers were due to reduced self-renewal of NSCs, such as radial glia, we measured the levels of the radial glia marker, Pax6, in mouse embryonic brains at 14.5 dpc. We found that Pax6 levels were decreased and the ventricular zone was thinner in the embryonic brains of Ubb KO mice compared to those of wild-type (WT) control mice. To determine whether the decreased self-renewal of Ubb KO NSCs was caused by cell-autonomous defects and not due to their microenvironment, we transplanted NSCs into WT mouse brains using a cannula system. In mouse brain sections, immunoreactivity of the NSC marker, nestin, was much lower in Ubb KO NSCs than in Ubb HT controls. Therefore, our data suggest that cell-autonomous defects, due to the disruption of Ubb, lead to a decrease in the self-renewal capacity of NSCs and may contribute to their dysregulated differentiation into neurons.

Systematic genetic analyses of GWAS data reveal an association between the immune system and insomnia

BACKGROUND

Previous studies have inferred a strong genetic component for insomnia. However, the etiology of insomnia is still unclear. The aim of the current study was to explore potential biological pathways, gene networks, and brain regions associated with insomnia.

METHODS

Using pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a large genome-wide association studies (GWASs) of insomnia symptoms (32,155 cases/26,973 controls), significant gene sets were tested for replication in other large GWASs of insomnia complaints (32,384 cases/80,622 controls). After the network analysis of unique genes within the replicated pathways, a gene set analysis for genes in each cluster/module of the enhancing neuroimaging genetics through meta-analysis GWAS data was performed for the volumes of the intracranial and seven subcortical regions.

RESULTS

A total of 31 of 1,816 Reactome pathways were identified and showed associations with insomnia risk. In addition, seven functionally and topologically interconnected clusters (clusters 0-6) and six gene modules (named Yellow, Blue, Brown, Green, Red, and Turquoise) were associated with insomnia. Moreover, significant associations were detected between common variants of the genes in Cluster 2 with hippocampal volume (p = 0.035; family wise error [FWE] correction) and the red module with intracranial volume (p = 0.047; FWE correction). Functional enrichment for genes in the Cluster 2 and the Red module revealed the involvement of immune responses, nervous system development, NIK/NF-kappaB signaling, and I-kappaB kinase/NF-kappaB signaling. Core genes (UBC, UBB, and UBA52) in the interconnected functional network were found to be involved in regulating brain development.

CONCLUSIONS

The current study demonstrates that the immune system and the hippocampus may play central roles in neurodevelopment and insomnia risk.

Irradiation of rainbow trout at early life stages results in a proteomic legacy in adult gills. Part A; proteomic responses in the irradiated fish and in non-irradiated bystander fish

Exposure to a single 0.5 Gy X-ray dose of eggs at 48 h after fertilisation (48 h egg), eyed eggs, yolk sac larvae (YSL) and first feeders induces a legacy effect in adult rainbow trout. This includes the transmission of a bystander effect to non-irradiated adult trout which had swam with the irradiated fish. The aim of this study was to investigate this legacy by analysing the gill proteome of these irradiated and bystander fish. Irradiation at all of the early life stages resulted in changes to proteins which play a key role in development but are also known to be anti-tumorigenic and anti-oxidant: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin, serum albumin 1 precursor (eyed eggs), clathrin heavy chain 1 isoform X10 (eyed eggs and first feeders), and actin-related protein 2/3 complex subunit 4 (first feeders), downregulation of pyruvate dehydrogenase, histone 1 (48 h egg), triosephosphate isomerase (TPI), collagen alpha-1(1) chain like proteins (YSL), pyruvate kinase PKM-like protein (YSL and first feeders), ubiquitin-40S ribosomal proteins S27 and eukaryotic translation initiation factor 4 A isoform 1B (first feeders). However irradiation of YSL and first feeders (post hatching early life stages) also induced proteomic changes which have a complex relationship with tumorigenesis or cancer progression; downregulation of alpha-1-antiprotease-like protein precursor, vigilin isoform X2 and nucleoside diphosphate kinase (YSL) and upregulation of hyperosmotic glycine rich protein (first feeders). In bystander fish some proteomic changes were similar to those induced by irradiation: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin (eyed eggs), actin-related protein 2/3 complex subunit 4, hyperosmotic glycine rich protein (first feeders), and downregulation of alpha-1-antiprotease-like protein, vigilin isoform X2, nucleoside diphosphate kinase (YSL), pyruvate kinase PKM-like protein and ubiquitin-40S ribosomal protein S27a-like (first feeders). Other proteomic changes were unique to bystander fish; downregulation of TPI, ubiquitin-40S ribosomal protein S2 (eyed egg), cofilin-2, cold-inducible RNA-binding protein B-like isoform X3 (YSL) and superoxide dismutase (first feeder), and upregulation of haemoglobin subunit alpha, collagen 1a1 precursor, apolipoprotein A-1-1 and A-1-2 precursor (first feeders). These bystander effect proteomic changes have been shown to be overwhelmingly anti-tumorigenic or protective of the fish gill.

Temporal downregulation of the polyubiquitin gene Ubb affects neuronal differentiation, but not maturation, in cells cultured in vitro

Reduced levels of cellular ubiquitin (Ub) pools due to disruption of the polyubiquitin gene Ubb lead to dysregulation of neural stem cell (NSC) differentiation and impaired neuronal maturation in cells isolated from Ubb^−/− mouse embryonic brains. However, it is currently unknown whether Ub is required for the specific stage of neuronal development or whether it plays a pleiotropic role throughout the process. To answer this question, we aimed to downregulate Ubb expression temporally during neuronal development, which could not be achieved in Ubb^−/− cells. Therefore, we exploited lentivirus-mediated knockdown (KD) of Ubb at different stages of neuronal development, and investigated their phenotypes. Here, we report the outcome of Ubb KD on two independent culture days in vitro (DIV): DIV1 and DIV7. We observed that NSCs did not differentiate properly via Ubb KD on DIV1, but the maturation of already differentiated neurons was intact via Ubb KD on DIV7. Intriguingly, Ubb KD activated Notch signaling when it had been suppressed, but exerted no effect when it had already been activated. Therefore, our study suggests that Ub plays a pivotal role in NSC differentiation to suppress Notch signaling, but not in the subsequent maturation stages of neurons that had already been differentiated.

Microarray analysis to identify the similarities and differences of pathogenesis between aortic occlusive disease and abdominal aortic aneurysm

Objectives Expression profile of GSE57691 was analyzed to identify the similarities and differences between aortic occlusive disease and abdominal aortic aneurysm. Methods The expression profile of GSE57691 was downloaded from Gene Expression Omnibus database, including 20 small abdominal aortic aneurysm samples, 29 large abdominal aortic aneurysm samples, 9 aortic occlusive disease samples, and 10 control samples. Using the limma package in R, the differentially expressed genes were screened. Followed by enrichment analysis was performed for the differentially expressed genes using database for annotation, visualization, and integrated discovery online tool. Based on string online tool and Cytoscape software, protein-protein interaction network and module analyses were carried out. Moreover, integrated TF platform database and Cytoscape software were used for constructing transcriptional regulatory networks. Results As a result, 1757, 354, and 396 differentially expressed genes separately were identified in aortic occlusive disease, large abdominal aortic aneurysm, and small abdominal aortic aneurysm samples. UBB was significantly enriched in proteolysis related pathways with a high degree in three groups. SPARCL1 was another gene shared by these groups and regulated by NFIA, which had a high degree in transcriptional regulatory network. ACTB, a significant upregulated gene in abdominal aortic aneurysm samples, could be regulated by CLIC4, which was significantly enriched in cell motions. ACLY and NFIB were separately identified in aortic occlusive disease and small abdominal aortic aneurysm samples, and separately enriched in lipid metabolism and negative regulation of cell proliferation. Conclusions The downregulated UBB, NFIA, and SPARCL1 might play key roles in both aortic occlusive disease and abdominal aortic aneurysm, while the upregulated ACTB might only involve in abdominal aortic aneurysm. ACLY and NFIB were specifically involved in aortic occlusive disease and small abdominal aortic aneurysm separately.

Regulation of REST levels overcomes dysregulation of neural stem cell differentiation caused by disruption of polyubiquitin gene Ubb

Reduced levels of cellular ubiquitin (Ub) caused by disruption of the polyubiquitin gene Ubb lead to dysregulated differentiation of neural stem/progenitor cells (NSCs) and apoptosis in cells cultured in vitro. However, the underlying mechanisms responsible for these phenotypes in Ub-deficient cells have not been studied extensively. In the present study, we found that levels of repressor element-1 silencing transcription factor (REST) are elevated in Ubb^-/- cells. To determine whether dysregulation of NSC differentiation is caused by the increased REST levels, we investigated the effect of reduced REST levels in Ubb^-/- cells. Rest knockdown was found to increase the expression of the neuronal marker βIII-tubulin (TUJ1) and restore the expression pattern of the early neuronal marker α-internexin (α-INX) in Ubb^-/- cells. Furthermore, Rest knockdown reduced Ub deficiency-induced apoptosis in cells cultured in vitro. Therefore, our study validates that cellular Ub levels are crucial for precise control of the levels of regulatory proteins such as REST during neurogenesis. We propose that regulation of Rest levels is a promising approach to overcome dysregulation of NSC differentiation caused by disruption of the polyubiquitin gene Ubb.

Effect of p62/SQSTM1 polyubiquitination on its autophagic adaptor function and cellular survival under oxidative stress induced by arsenite

Oxidative stress induced by arsenite [As(III)] affects protein folding and results in increased levels of misfolded proteins or protein aggregates. Accumulation of misfolded protein aggregates may act as a cue signal for the oligomerization of the autophagic adaptor protein p62, which facilitates recognition of misfolded protein aggregates that are polyubiquitinated with K63 linkages. However, as the autophagic flux is impaired under exposure to As(III), p62 oligomers cannot be cleared by autophagy and accumulate as aggregates with Keap1. This results in the sequestration of Keap1 and the stabilization of Nrf2, which activates the non-canonical Nrf2-Keap1 pathway as an antioxidant response. In this study, we found that polyubiquitination of p62 itself increased upon exposure to As(III) to prevent further oligomerization of p62 and to increase the availability of functional free monomeric p62. We also found that monomeric p62 could also interact with ubiquitinated proteins and that the forced dimerization of p62 was sufficient to increase the interactions with ubiquitinated proteins, probably polyubiquitinated with K63 linkages. Upon exposure to As(III), (1) inability to form oligomeric p62 because of a mutation in the PB1 dimerization domain, or (2) reduced capability to generate monomeric p62 owing to diminished polyubiquitination of p62 itself, resulted in reduced viability of cells. Therefore, upon exposure to As(III), p62 initially needs to form oligomers to activate an antioxidant response pathway. Subsequently, p62 is polyubiquitinated to prevent further oligomerization and ensure the availability of free p62 monomers. We propose that the polyubiquitination of p62 under exposure to As(III) plays an important role in overcoming the impaired autophagic flux by regulating the oligomerization status of p62.

Effect of cellular ubiquitin levels on the regulation of oxidative stress response and proteasome function via Nrf1

The polyubiquitin genes Ubb and Ubc are upregulated under oxidative stress induced by arsenite [As(III)]. However, the role of ubiquitin (Ub) under As(III) exposure is not known in detail. In a previous study, we showed that the reduced viability observed in Ubc^-/- mouse embryonic fibroblasts under As(III) exposure was not due to dysregulation of the Nrf2-Keap1 pathway, which prompted us to investigate another NFE2 family protein, nuclear factor erythroid 2-related factor 1 (Nrf1). In this study, we found that Ub deficiency due to Ubc knockdown in N2a cells reduced cell viability and proteasome activity under As(III) exposure. Furthermore, mRNA levels of the proteasome subunit Psma1 were also reduced. In addition, Ub deficiency led to the nuclear accumulation of the p65 isoform of Nrf1 under As(III) exposure. Interestingly, the overexpression of p65-Nrf1 recapitulated the phenotypes of Ub-deficient N2a cells under As(III) exposure. On the other hand, Nrf1 knockdown suppressed the death of Ub-deficient N2a cells upon exposure to As(III). Therefore, the levels of p65-Nrf1 may play an important role in the maintenance of cell viability under oxidative stress induced by As(III).

Disruption of polyubiquitin gene Ubc leads to attenuated resistance against arsenite-induced toxicity in mouse embryonic fibroblasts

The polyubiquitin gene Ubc is upregulated under oxidative stress induced by arsenite [As(III)]. However, the detailed mechanism of Ubc upregulation and the exact role of ubiquitin (Ub) to protect cells against As(III)-induced toxicity remain unknown. Here, we found that Ubc-/- mouse embryonic fibroblasts (MEFs) exhibited reduced viability under As(III) exposure, although the Nrf2-Keap1 pathway was activated as a cytoprotective response. Intriguingly, due to the reduced polyubiquitination and delayed onset of degradation of Nrf2 in Ubc-/- MEFs, the basal expression levels of Nrf2 target genes were elevated. As(III)-induced accumulation of Ub conjugates occurred in an Nrf2-independent manner, probably due to cellular stress conditions, including reduced proteasomal activity. Increased cellular Ub levels were essential to polyubiquitinate misfolded proteins generated under As(III) exposure and to degrade them by the proteasome. However, when cellular Ub levels decreased, these misfolded proteins were not efficiently polyubiquitinated, but rather accumulated as large protein aggregates inside the cells, causing cytotoxicity. Furthermore, increased activity of the autophagic pathway to clear these aggregates was not observed in Ubc-/- MEFs. Therefore, reduced viability of Ubc-/- MEFs under As(III) exposure may not be due to dysregulation of the Nrf2-Keap1 pathway, but mostly to reduced efficacy to polyubiquitinate and degrade misfolded protein aggregates.