The immunoproteasome, the 20S proteasome and the PA28αβ proteasome regulator are oxidative-stress-adaptive proteolytic complexes

Oxidized cytoplasmic and nuclear proteins are normally degraded by the proteasome, but accumulate with age and disease. We demonstrate the importance of various forms of the proteasome during transient (reversible) adaptation (hormesis), to oxidative stress in murine embryonic fibroblasts. Adaptation was achieved by 'pre-treatment' with very low concentrations of H2O2, and tested by measuring inducible resistance to a subsequent much higher 'challenge' dose of H2O2. Following an initial direct physical activation of pre-existing proteasomes, the 20S proteasome, immunoproteasome and PA28αβ regulator all exhibited substantially increased de novo synthesis during adaptation over 24?h. Cellular capacity to degrade oxidatively damaged proteins increased with 20S proteasome, immunoproteasome and PA28αβ synthesis, and was mostly blocked by the 20S proteasome, immunoproteasome and PA28 siRNA (short interfering RNA) knockdown treatments. Additionally, PA28αβ-knockout mutants achieved only half of the H2O2-induced adaptive increase in proteolytic capacity of wild-type controls. Direct comparison of purified 20S proteasome and immunoproteasome demonstrated that the immunoproteasome can selectively degrade oxidized proteins. Cell proliferation and DNA replication both decreased, and oxidized proteins accumulated, during high H2O2 challenge, but prior H2O2 adaptation was protective. Importantly, siRNA knockdown of the 20S proteasome, immunoproteasome or PA28αβ regulator blocked 50-100% of these adaptive increases in cell division and DNA replication, and immunoproteasome knockdown largely abolished protection against protein oxidation.     

To misfold or to lose structure?: Detection and degradation of oxidized proteins by the 20S proteasome

Aggregation of proteins damaged by stress is often a causal factor of cell death. To prevent aggregation, eukaryotic cells rapidly degrade damaged proteins by engaging two types of proteasomes. The first type is the 26S proteasome (26SP) which is composed of a cylindrical proteolytic core—the 20S proteasome (20SP)—and one or two regulatory particles (RPs) that interact with ubiquitinated proteins. The second type is the free 20SP which mediates ubiquitin-independent proteolysis. We have recently shown that loss of RP function in Arabidopsis leads to an expected decrease in 26SP-dependent protein degradation and hypersensitivity to stresses that induce protein misfolding. Surprisingly, RP mutants have increased 20SP activity and tolerance to oxidative stress. This finding suggests that misfolded proteins carry one type of degradation signal that steers them to ubiquitination enzymes and the 26SP, while oxidatively damaged proteins carry another that guides them directly to the 20SP for degradation. Here we suggest that protein oxidation induces the formation of unstructured regions that serve as targeting signals for 20SP-dependent proteolysis.Key words: 20S proteasome, misfolded proteins, oxidized proteins, ubiquitin-independent proteolysis, unstructured regionsProteasomes are an essential component of the quality-control system that limits the accumulation of non-functional proteins in the cell.^1–4 A protein can be rendered non-functional by mutations, translational and folding errors, and adverse conditions such as heat shock and oxidative stress. These proteins decrease the efficiency of metabolic pathways not only because of their loss of function, but also because of the deleterious gain-of-function effects generally known as proteotoxicity.^1–4 Until recently, it was widely accepted that the detection and degradation of all non-functional proteins is initiated by their loss of native tertiary structure followed by misfolding. Misfolding is believed to expose hydrophobic regions that form interaction domains for chaperones, which are in turn bound to ubiquitin ligases that label the target for 26SP-dependent proteolysis.^5–9 Thus, the degradation of proteins that have lost their native conformation was considered to be an ubiquitin (Ub)- and 26SP-dependent process (Fig. 1).Open in a separate windowFigure 1Model for the degradation of damaged proteins. (A) Stresses such as heat shock or the incorporation of amino acid analogues induce protein misfolding. If for example, a globular protein is misfolded, its hydrophobic core will be exposed to the cytoplasm. These hydrophobic regions can bind chaperones that either repair the misfolded protein or shuttle it to the ubiquitination enzymes and the 26SP. (B) Protein oxidation leads to a partial loss of secondary structure without disrupting the overall folding pattern of the protein, resulting in flexible, unstructured regions. These regions serve as degradation signals for the Ub-independent 20SP pathway.However, a number of studies have shown that the degradation of proteins damaged by oxidative stress follows another route: oxidized proteins are degraded by the 20SP in a Ub-independent manner.^5–7,10 We have recently shown that this proteolysis pathway is important for oxidative stress tolerance in plants. Loss of function of the Arabidopsis RP subunits RPT2a, RPN10 and RPN12a reduces 26SP function and leads to an expected decrease in Ub-dependent proteolysis.^11–14 Unexpectedly, all three RP mutants have increased 20SP activity, which is probably caused by the stabilization of an activator of proteasome biogenesis that is normally degraded by the 26SP.¹¹ This shift in proteasome activity leads to increased oxidized protein turnover and oxidative stress tolerance, but also to decreased tolerance to stresses that are known to cause protein misfolding.¹¹ Thus, the 26SP in Arabidopsis is needed for the removal of misfolded proteins, and the 20SP is essential for the degradation of oxidized proteins.This differential degradation of damaged proteins implies that plant cells have distinct recognition mechanisms for misfolded and oxidized proteins, and that oxidation leads to the formation of a specific degradation signal that channels the oxidized proteins directly to the 20SP. Nevertheless, it has been suggested that the proteolysis of oxidized proteins also depends on misfolding and exposure of hydrophobic regions that serve as recognition sites for either the 20SP itself or for specific chaperonins that bind the 20SP.^5–7,10,15 If the recognition of proteasomal targets is specific, then—according to the current theory—heat shock and oxidative stress would expose specific types of hydrophobic degradation signals in any cellular protein. These qualitatively different hydrophobic regions would lead either to ubiquitination and 26SP-dependent degradation or to a direct interaction with the 20SP. While we cannot exclude this, it is hard to envision how a random process such as misfolding would produce discernable degradation signals dependent on whether the denaturation was caused by heat shock or by oxidation. An alternative explanation is that the recognition of oxidized proteins does not depend on misfolding.How would oxidized proteins then be targeted to the 20SP? Today we know of some functional proteins that are degraded by the 20SP in a Ub-independent manner, and all these characterized 20SP targets have regions that lack secondary structure.^10,16 The native unstructured regions or intrinsically disordered regions give conformational plasticity to a protein and allow it to form a complex with different partners.^17,18 The unstructured regions are also thought to serve as initiation sites for proteolysis.¹⁹ These findings are a starting point for the “degradation by default” theory which states that many proteins in their native conformation contain unstructured regions that make them inherently unstable and target them to the Ub-independent 20SP pathway.¹⁰ Such proteins tend to be stabilized by forming complexes in which the unstructured regions are masked by other polypeptides. Since oxidized proteins are processed by the 20SP, their common degradation signal could also be an intrinsically disordered region (Fig. 1). Thus, protein oxidation—at least mild protein oxidation⁶—would lead to the formation of flexible peptide stretches (i.e., unstructured regions) rather than to protein misfolding (i.e., unfolding and non-native refolding that exposes otherwise sequestered hydrophobic residues). This hypothesis is supported by a study of the 20SP-dependent degradation of oxidized calmodulin (CaM).²⁰ Oxidation of CaM leads to a significant increase in its 20SP-dependent and Ub-independent degradation. In vitro studies revealed a positive correlation between decreased secondary structure (i.e., increased flexibility) and proteolysis rate, and no correlation between changes in surface hydrophobicity and CaM stability.²⁰There is another paradox concerning 20SP-dependent proteolysis of oxidized proteins. The 20SP is a barrel-shaped particle composed of two α and two β rings in an α7β7b7β7 configuration.²¹ Proteolytic activity is confined to the β rings and is broad range, so that it degrades any target into oligopeptides of 3–25 amino acids in length. To be degraded, targets must not only be recognized by the 20SP, but must also enter into the proteolytic chamber through a constriction in the α rings known as the α-annulus. In 26SP-dependent proteolysis, this entry point is opened by the action of a ring of AAA ATPases from the RP.²¹ However, this entrance gate of the free 20SP is closed and restricts random proteolysis. How then do oxidized proteins enter the proteolytic chamber? It has been shown that some natively unstructured proteins can open the gates possibly by acting as chaotropes and by causing subunit residues to become disordered.²² This then could also be the entry mechanism for oxidized proteins.In conclusion, analyses of Arabidopsis proteasome mutants with decreased Ub-dependent proteolysis reveals that the 20SP-dependent “degradation by the default” pathway is operational in plants and is important for oxidative stress tolerance. However, it remains to be shown whether indeed the unstructured regions, either innate or formed by the action of free radicals, guide proteins to the 20SP and specifically cause the opening of the α-annulus. The identities of native 20SP targets in plants also await further studies.     

REGγ proteasome mediates degradation of the ubiquitin ligase Smurf1

The ubiquitin ligase Smad ubiquitination regulatory factor 1 (Smurf1) targets many proteins including Smad1/5 for ubiquitin-dependent proteasomal degradation. However, how Smurf1 is degraded remains unclear. Here we show that REGγ, an activator for the 20S proteasome-mediated protein degradation, interacts with Smurf1 and mediates its degradation. We provide evidence that depletion of REGγ stabilizes Smurf1 whereas overexpression of REGγ promotes the degradation of Smurf1. Interestingly both Smurf2 and Smurf1 are destabilized by the REGγ proteasome while the other members of Neural precursor cell-expressed developmentally downregulated gene 4 family were not affected. More importantly, we found that the REGγ proteasome-mediated degradation of Smurf1 results in degradation of Smad5. These findings reveal that the REGγ-proteasome targets a ubiquitin ligase for protein degradation.

Structured summary

MINT-7894509: CKIP (uniprotkb:Q53GL0) binds (MI:0407) to Smurf1 (uniprotkb:Q9HCE7) by pull down (MI:0096)MINT-7894494: REG gamma (uniprotkb:P61289) binds (MI:0407) to Smurf1 (uniprotkb:Q9HCE7) by pull down (MI:0096)MINT-7894523, MINT-7894543, MINT-7894481: REG gamma (uniprotkb:P61289) physically interacts (MI:0915) with Smurf1 (uniprotkb:Q9HCE7) by anti tag coimmunoprecipitation (MI:0007)MINT-7894558: Smurf1 (uniprotkb:Q9HCE7) physically interacts (MI:0915) with REG gamma (uniprotkb:P61289) by two hybrid (MI:0018)     

Involvement of the nuclear proteasome activator PA28γ in the cellular response to DNA double-strand breaks

The DNA damage response (DDR) is a complex signaling network that leads to damage repair while modulating numerous cellular processes. DNA double-strand breaks (DSBs)—a highly cytotoxic DNA lesion—activate this system most vigorously. The DSB response network is orchestrated by the ATM protein kinase, which phosphorylates key players in its various branches. Proteasome-mediated protein degradation plays an important role in the proteome dynamics following DNA damage induction. Here, we identify the nuclear proteasome activator PA28γ (REGγ; PSME3) as a novel DDR player. PA28γ depletion leads to cellular radiomimetic sensitivity and a marked delay in DSB repair. Specifically, PA28γ deficiency abrogates the balance between the two major DSB repair pathways—nonhomologous end-joining and homologous recombination repair. Furthermore, PA28γ is found to be an ATM target, being recruited to the DNA damage sites and required for rapid accumulation of proteasomes at these sites. Our data reveal a novel ATM-PA28γ-proteasome axis of the DDR that is required for timely coordination of DSB repair.     

Involvement of the nuclear proteasome activator PA28γ in the cellular response to DNA double-strand breaks

The DNA damage response (DDR) is a complex signaling network that leads to damage repair while modulating numerous cellular processes. DNA double-strand breaks (DSBs), a highly cytotoxic DNA lesion, activate this system most vigorously. The DSB response network is orchestrated by the ATM protein kinase, which phosphorylates key players in its various branches. Proteasome-mediated protein degradation plays an important role in the proteome dynamics following DNA damage induction. Here, we identify the nuclear proteasome activator PA28γ (REGγ; PSME3) as a novel DDR player. PA28γ depletion leads to cellular radiomimetic sensitivity and a marked delay in DSB repair. Specifically, PA28γ deficiency abrogates the balance between the two major DSB repair pathways—nonhomologous end-joining and homologous recombination repair. Furthermore, PA28γ is found to be an ATM target, being recruited to the DNA damage sites and required for rapid accumulation of proteasomes at these sites. Our data reveal a novel ATM-PA28γ-proteasome axis of the DDR that is required for timely coordination of DSB repair.Key words: genomic stability, DNA repair, double-strand breaks, ATM, proteasome, PA28γ (PSME3)     

The roles of 3′-exoribonucleases and the exosome in trypanosome mRNA degradation

The degradation of eukaryotic mRNAs can be initiated by deadenylation, decapping, or endonuclease cleavage. This is followed by 5′–3′ degradation by homologs of Xrn1, and/or 3′–5′ degradation by the exosome. We previously reported that, in African trypanosome Trypanosoma brucei, most mRNAs are deadenylated prior to degradation, and that depletion of the major 5′–3′ exoribonuclease XRNA preferentially stabilizes unstable mRNAs. We now show that depletion of either CAF1 or CNOT10, two components of the principal deadenylation complex, strongly inhibits degradation of most mRNAs. RNAi targeting another deadenylase, PAN2, or RRP45, a core component of the exosome, preferentially stabilized mRNAs with intermediate half-lives. RRP45 depletion resulted in a 5′ bias of mRNA sequences, suggesting action by a distributive 3′–5′ exoribonuclease. Results suggested that the exosome is involved in the processing of trypanosome snoRNAs. There was no correlation between effects on half-lives and on mRNA abundance.     

Purification and separation of the 20S immunoproteasome from the constitutive proteasome and identification of the subunits by LC–MS

The proteasome is a multicatalytic protease complex present in all eukaryotic cells, which plays a critical role in regulating essential cellular processes. During the immune response to pathogens, stimulation by γ interferon induces the production of a special form of proteasome, the immunoproteasome. Inappropriate increase of proteosomal activity has been linked to inflammatory and autoimmune diseases. Selective inhibition of the immunoproteasome specific LMP7 subunit was shown to block inflammatory cytokine secretion in human PBMC, thus making the immunoproteasome an interesting target to fight autoimmune diseases. This paper describes a method for purification and separation of the 20S immunoproteasomes from the constitutive proteasome, which is ubiquitously present in all cells, based on hydrophobic interaction chromatography. The purified immunoproteasome showed several bands, between 20–30 kDa, when subjected to polyacrylamide gel electrophoresis under denaturing conditions. The purified proteasome complexes had a molecular mass of approximately 700 kDa as estimated by gel filtration. Identification of the catalytic subunits in the immunoproteasomes was performed in Western blot with antibodies directed specifically against either the constitutive or the immunoproteasome subunits. The purified immunoproteasome possessed all three protease activities associated with the proteasome complex. LC/MS analysis confirmed the presence of the three immunoproteasome catalytic subunits in the purified immunoproteasome.     

Fluorescent detection of α-aminoadipic and γ-glutamic semialdehydes in oxidized proteins

The oxidative modification of proteins is believed to play a critical role in the etiology and/or progression of several diseases. α-Aminoadipic semialdehyde (AAS) and γ-glutamic semialdehyde (GGS) residues represent major oxidized amino acids generated in oxidized proteins. This paper describes a novel procedure for the specific and sensitive determination of AAS and GGS after their reductive amination with sodium cyanoborohydride and p-aminobenzoic acid, a fluorescence reagent, to their corresponding derivatives, followed by a high-performance liquid chromatography (HPLC) analysis. This fluorescent labeling of protein-associated aldehyde moieties is a simple and accurate technique that may be widely used to reveal increased levels of oxidatively modified proteins with reactive oxygen species during aging and disease.     

REGγ proteasome activator is involved in the maintenance of chromosomal stability

REGγ is a member of the 11S regulatory particle that activates the 20S proteasome. Studies in REGγ deficient mice indicated an additional role for this protein in cell cycle regulation and proliferation control. In this paper we demonstrate that REGγ protein is equally expressed throughout the cell cycle, but undergoes a distinctive subcellular localization at mitosis. Thus, while in interphase cells REGγ is nuclear, in telophase cells it localizes on chromosomes, suggesting a role in mitotic progression. Furthermore, we found that REGγ overexpression weakens the mitotic arrest induced by spindle damage, allowing premature exit from mitosis, whereas REGγ depletion has the opposite effect, thus reflecting a new REGγ function, unrelated to its role as proteasome activator. Additionally, we found that primary cells from REGγ-/- mice and human fibroblasts with depleted expression of REGγ or overexpressing a dominant negative mutant unable to activate the 20S proteasome, demonstrated a marked aneuploidy (chromosomal gains and losses), supernumerary centrosomes and multipolar spindles. These findings thus underscore a previously uncharacterized function of REGγ in centrosome and chromosomal stability maintenance.     

Does rapid oligomerization of hepatitis B envelope proteins play a role in resistance to proteasome degradation and enhance chronicity?

This review discusses the nature of hepatitis B and C chronicity from a virological perspective. Work described in the literature and our in vitro studies of HBV polypeptide morphogenesis lead us to speculate about a role for HBsAg complex formation in immune evasion that may be especially important during the initial period of infection. Briefly, although viral structural proteins do eventually provide epitopes recognized by the host, we suggest that these HBs Ag complexes, which may themselves be refractory to proteasomal degradation, are an important way by which the virus shields its epitopes and evades early recognition by the cellular immune system. This suggests a central strategy by which the virus has evolved, structurally, to enable the establishment of persistent infection of its host. The concept offers an explanation for the nearly unidirectional and rapid kinetics whereby HBV proteins form multimers and generate a surplus of viral structures that have not been thought to serve any useful structural purpose.     

Differential roles of estrogen receptors α and β in control of B-cell maturation and selection

It is clear that estrogen can accelerate and exacerbate disease in some lupus-prone mouse strains. It also appears that estrogen can contribute to disease onset or flare in a subset of patients with lupus. We have previously shown estrogen alters B-cell development to decrease lymphopoiesis and increase the frequency of marginal zone B cells. Furthermore, estrogen diminishes B-cell receptor signaling and allows for the increased survival of high-affinity DNA-reactive B cells. Here, we analyze the contribution of estrogen receptor α or β engagement to the altered B-cell maturation and selection mediated by increased exposure to estrogen. We demonstrate that engagement of either estrogen receptor α or β can alter B-cell maturation, but only engagement of estrogen receptor α is a trigger for autoimmunity. Thus, maturation and selection are regulated differentially by estrogen. These observations have therapeutic implications.     

Checkpoints in ER-associated degradation: excuse me, which way to the proteasome?

The failure of secreted proteins to fold results in their retrotranslocation from the endoplasmic reticulum (ER) and degradation by the proteasome in a process called "ER-associated degradation" (ERAD). Two recent studies indicate that ERAD substrates are targeted to different pathways depending on the topology of the substrate and the subcellular location of the misfolded domain.     

Preassembly and ligand-induced restructuring of the chains of the IFN-γ receptor complex： the roles of Jak kinases, Statl and the receptor chains

We previously demonstrated using noninvasive technologies that the interferon-gamma （IFN-γ） receptor complex is preassembled [ 1 ]. In this report we determined how the receptor complex is preassembled and how the ligand-mediated conformational changes occur. The interaction of Statl with IFN-γR1 results in a conformational change localized to IFN- γR1. Jakl but not Jak2 is required for the two chains of the IFN-γ receptor complex （IFN-γR1 and IFN-γR2） to interact; however, the presence of both Jakl and Jak2 is required to see any ligand-dependant conformational change. Two IFN- γR2 chains interact through species-specific determinants in their extracellular domains. Finally, these determinants also participate in the interaction of IFN-γR2 with IFN-γR1. These results agree with a detailed model of the IFN-γ receptor that requires the receptor chains to be pre-associated constitutively for the receptor to be active.     

Polymorphisms and diversity of T-cell receptor-γ proteins expressed in mouse spleen

Bulk populations of T-cell receptor (Tcr) -expressing splenocytes from different inbred strains of mice were examined for the diversity of Tcr proteins. Immunoprecipitations with anti-C1/2, anti-C4, and anti-V1 sera demonstrated that splenocytes from B10.BR, C57BL/6, and C57L strains of mice expressed the same array of Tcr proteins, namely V1-C2, V1-C4, and V2-C1, although the Tcr heterodimers observed for each of these strains were biochemically distinct. Examination of bulk splenic Tcr heterodimers from several other inbred strains of mice demonstrated that each of the strains could be categorized into one of three basic phenotypes. For several reasons, the differences observed between the strains appeared to be solely dependent on polymorphisms of the Tcrg loci. First, F₁ mice co-expressed both parental Tcr phenotypes. Second, the distinguishing polymorphism between mice of phenotype 1 and phenotypes 2 or 3 was due to the presence of an N-linked glycosylation site within the Tcrg-C1 gene segment, previously described for BALB.B and C57BL/6 Tcrg-C1 genes. Finally, the V1-C4 polymorphism between mice of phenotype 3 and phenotypes 1 or 2 was due to differences in core protein size. Furthermore, the three defined Tcr chains were expressed independently of the major histocompatibility complex (MHC) haplotype. Although no striking qualitative differences in Tcr heterodimers were observed between strains (including those with autoimmune disorders), a quantitative difference in the relative amount of C4-encoded proteins was observed on Tcr splenocytes from both newborn euthymic and adult athymic mice when compared to adult Tcr splenocytes from euthymic mice. These results demonstrate that genetic polymorphisms exist among different mouse strains and suggest that selective developmental pressures may govern Tcr expression. Offprint requests to: J. A. Bluestone     

Nrf2-dependent induction of proteasome and Pa28αβ regulator are required for adaptation to oxidative stress

The ability to adapt to acute oxidative stress (e.g. H(2)O(2), peroxynitrite, menadione, and paraquat) through transient alterations in gene expression is an important component of cellular defense mechanisms. We show that such adaptation includes Nrf2-dependent increases in cellular capacity to degrade oxidized proteins that are attributable to increased expression of the 20 S proteasome and the Pa28αβ (11 S) proteasome regulator. Increased cellular levels of Nrf2, translocation of Nrf2 from the cytoplasm to the nucleus, and increased binding of Nrf2 to antioxidant response elements (AREs) or electrophile response elements (EpREs) in the 5'-untranslated region of the proteasome β5 subunit gene (demonstrated by chromatin immunoprecipitation (or ChIP) assay) are shown to be necessary requirements for increased proteasome/Pa28αβ levels, and for maximal increases in proteolytic capacity and stress resistance; Nrf2 siRNA and the Nrf2 inhibitor retinoic acid both block these adaptive changes and the Nrf2 inducers DL-sulforaphane, lipoic acid, and curcumin all replicate them without oxidant exposure. The immunoproteasome is also induced during oxidative stress adaptation, contributing to overall capacity to degrade oxidized proteins and stress resistance. Two of the three immunoproteasome subunit genes, however, contain no ARE/EpRE elements, and Nrf2 inducers, inhibitors, and siRNA all have minimal effects on immunoproteasome expression during adaptation to oxidative stress. Thus, immunoproteasome appears to be (at most) minimally regulated by the Nrf2 signal transduction pathway.     

Biogenic production of DMSP and its degradation to DMS—their roles in the global sulfur cycle

Dimethyl sulfide(DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate(DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified.Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage.Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.