The proteasome activator 11 S REG (PA28) and class I antigen presentation. Biochem J. 2000;345 Pt1:1-15. [PMID: 10600633 DOI: 10.1042/0264-6021:3450001]

PA28γ-20S proteasome is a proteolytic complex committed to degrade unfolded proteins

PA28γ is a nuclear activator of the 20S proteasome that, unlike the 19S regulatory particle, stimulates hydrolysis of several substrates in an ATP- and ubiquitin-independent manner and whose exact biological functions and molecular mechanism of action still remain elusive. In an effort to shed light on these important issues, we investigated the stimulatory effect of PA28γ on the hydrolysis of different fluorogenic peptides and folded or denatured full-length proteins by the 20S proteasome. Importantly, PA28γ was found to dramatically enhance breakdown rates by 20S proteasomes of several naturally or artificially unstructured proteins, but not of their native, folded counterparts. Furthermore, these data were corroborated by experiments in cell lines with a nucleus-tagged myelin basic protein. Finally, mass spectrometry analysis of the products generated during proteasomal degradation of two proteins demonstrated that PA28γ does not increase, but rather decreases, the variability of peptides that are potentially suitable for MHC class I antigen presentation. These unexpected findings indicate that global stimulation of the degradation of unfolded proteins may represent a more general feature of PA28γ and suggests that this proteasomal activator might play a broader role in the pathway of protein degradation than previously believed.

The immunoproteasome and viral infection: a complex regulator of inflammation

During viral infection, proper regulation of immune responses is necessary to ensure successful viral clearance with minimal host tissue damage. Proteasomes play a crucial role in the generation of antigenic peptides for presentation on MHC class I molecules, and thus activation of CD8 T cells, as well as activation of the NF-κB pathway. A specialized type of proteasome called the immunoproteasome is constitutively expressed in hematopoietic cells and induced in non-immune cells during viral infection by interferon signaling. The immunoproteasome regulates CD8 T cell responses to many viral epitopes during infection. Accumulating evidence suggests that the immunoproteasome may also contribute to regulation of proinflammatory cytokine production, activation of the NF-κB pathway, and management of oxidative stress. Many viruses have mechanisms of interfering with immunoproteasome function, including prevention of transcriptional upregulation of immunoproteasome components as well as direct interaction of viral proteins with immunoproteasome subunits. A better understanding of the role of the immunoproteasome in different cell types, tissues, and hosts has the potential to improve vaccine design and facilitate the development of effective treatment strategies for viral infections.

Proteomic analysis of exosomes derived from human lymphoma cells

Background

Exosomes secreted by tumor cells contain specific antigens that may have immunotherapeutic purposes. The aim of this study was to characterize the proteomic content of lymphoma cell-derived exosomes (LCEXs).

Methods

In this study, exosomes derived from Raji cells (EXO_Raji) were purified and proteins of EXO_Raji were separated by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Protein bands were identified by mass spectrometry. The protein components of EXO_Raji were analyzed using shotgun technology, and the function proteins of EXO_Raji were defined and described using the Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.

Results

A total of 197 proteins were identified in EXO_Raji; 139 proteins were also identified in Raji cells, showing an overlap of 70.56% of the total proteins in EXO_Raji. Interestingly, the remaining 58 proteins were unique to EXO_Raji. The GO database and KEGG were used to define and describe the function of proteins. The data showed that some important proteins involved in antigen procession and presentation as well as cell migration and adhesion were also identified in EXO_Raji, such as MHC-I and II, HSC70, HSP90, and ICMA-1.

Conclusions

LCEXs express a discrete set of proteins involved in antigen presentation and cell migration and adhesion, suggesting that LCEXs play an important role in the regulation of immunity and interaction between lymphoma cells and their microenvironment. LCEXs harbor most of the proteins of lymphoma cells and could be one of the sources of lymphoma-associated antigens for immunotherapeutic purposes.

Proteasome subtypes and regulators in the processing of antigenic peptides presented by class I molecules of the major histocompatibility complex

The proteasome is responsible for the breakdown of cellular proteins. Proteins targeted for degradation are allowed inside the proteasome particle, where they are cleaved into small peptides and released in the cytosol to be degraded into amino acids. In vertebrates, some of these peptides escape degradation in the cytosol, are loaded onto class I molecules of the major histocompatibility complex (MHC) and displayed at the cell surface for scrutiny by the immune system. The proteasome therefore plays a key role for the immune system: it provides a continued sampling of intracellular proteins, so that CD8-positive T-lymphocytes can kill cells expressing viral or tumoral proteins. Consequently, the repertoire of peptides displayed by MHC class I molecules at the cell surface depends on proteasome activity, which may vary according to the presence of proteasome subtypes and regulators. Besides standard proteasomes, cells may contain immunoproteasomes, intermediate proteasomes and thymoproteasomes. Cells may also contain regulators of proteasome activity, such as the 19S, PA28 and PA200 regulators. Here, we review the effects of these proteasome subtypes and regulators on the production of antigenic peptides. We also discuss an unexpected function of the proteasome discovered through the study of antigenic peptides: its ability to splice peptides.

PA28αβ: the enigmatic magic ring of the proteasome?

PA28αβ is a γ-interferon-induced 11S complex that associates with the ends of the 20S proteasome and stimulates in vitro breakdown of small peptide substrates, but not proteins or ubiquitin-conjugated proteins. In cells, PA28 also exists in larger complexes along with the 19S particle, which allows ATP-dependent degradation of proteins; although in vivo a large fraction of PA28 is present as PA28αβ-20S particles whose exact biological functions are largely unknown. Although several lines of evidence strongly indicate that PA28αβ plays a role in MHC class I antigen presentation, the exact molecular mechanisms of this activity are still poorly understood. Herein, we review current knowledge about the biochemical and biological properties of PA28αβ and discuss recent findings concerning its role in modifying the spectrum of proteasome's peptide products, which are important to better understand the molecular mechanisms and biological consequences of PA28αβ activity.

[Proteasomes on thyroid tissue allotransplantation under induction of donor specific tolerance in rats]

The proteasomes in the liver of August rats (RT1C) were investigated 30 days after the allotransplantation of Wistar rat (RT1u) thyroid tissue under renal capsule with/without induction of donor specific tolerance by donor splenocyte intraportal administration. The level of the total proteasome pool, immune proteasomes containing the LMP2 and/or LMP7 subunits, proteasome 19S- and 11S-regulators was defined. The intact and sham-operated August rats were used as control groups. The level of all immune proteasome forms and 11S regulator increased while the level of the total proteasome pool and 19S regulator decreased in the liver of experimental animals compared to the control groups that indicated changes of liver functional state after transplantation. The 19S/11S ratio increased in the liver of non-tolerated rats compared to tolerated animals. In the liver of tolerated rats with survived transplants, the quantity of mononuclear cells, expressing the immune subunit LMP2, greatly increased in comparison with control and non-tolerated animals. Study of the survived transplants showed the increase of the ratio of LMP2/LMP7 immune subunits and 19S/11S regulators in them compared to the tissue replacing the rejected transplants. In the control intact thyroid tissue, the immune proteasomes were almost not revealed, while 19S/11S ratio was maximal. Thus, the development of the immune reaction or its suppression is accompanied by change of the balance between different proteasome forms. The immune subunit LMP7 and 11S regulator are connected with the response against donor tissue. On the contrary, the immune subunit LMP2 and 19S regulator are likely to be important for the immune tolerance development and survived tissue functioning. The low content of the immune proteasomes in the follicle cells was found by immunofluorescence assay. The formation of antigens for major histocompatibility complex class I molecules was impaired by low immune proteasome content that led to immunological tolerance to hormone-producing follicle cells.

Genomic structural characterization and transcriptional expression analysis of proteasome activator PA28α and PA28β subunits from Oplegnathus fasciatus

Proteasomes are multicatalytic subunit complexes involved in the degradation of cytosolic proteins and antigen presentation. In this study, we have characterized the alpha and beta subunits of proteasome activator complex from rock bream at the molecular level. RbPA28α and RbPA28β possessed the characteristic features of the subunits identified from mammals and teleosts. The RbPA28α and RbPA28β proteasome subunits contained a proline-rich motif (Region A), subunit-specific insert in the region corresponding to the KEKE motif of the known PA28α (Region B), conserved activation loop (Region C), a potential protein kinase C recognition site (Region D) and a highly homologous C-terminal region (Region E) among all three PA28 subunits. Multiple sequence alignment and pairwise alignment revealed that RbPA28α and RbPA28β proteins shared high homology with the teleosts and mammals. RbPA28α and RbPA28β genome possessed 11 exons interrupted by 10 introns. In silico promoter analysis of RbPA28α and RbPA28β revealed various transcription factor-binding sites displaying their regulation under various stress conditions. Tissue distribution profiling showed a higher expression in blood and gills. Transcriptional expression analysis of RbPA28α and RbPA28β showed up-regulation in the immune tissues following LPS and poly I:C challenges, providing further evidence for the immunological role of RbPA28α and RbPA28β.

Molecular and functional characterization of a putative PA28γ proteasome activator orthologue in Schistosoma mansoni

PA28γ is a proteasome activator involved in the regulation of the cellular proliferation, differentiation and growth. In the present study, we identified and characterized a cDNA from Schistosoma mansoni exhibiting significant homology to PA28γ of diverse taxa ranging from mammals (including humans) to simple invertebrates. Designated SmPA28γ, this transcript has a 753bp predicted ORF encoding a protein of 250 amino acid residues. Alignment of SmPA28γ with multiple PA28γ orthologues revealed an average similarity of ~40% among the investigated organisms, and 90% similarity with PA28γ from Schistosoma japonicum. In addition, phylogenetic analysis demonstrated a close linkage between SmPA28γ to its sister group that contains well-characterized PA28γ sequences from Drosophila spp., as well as sharing the same branch with PA28γ from S. japonicum. Gene expression profiling of SmPA28γ using real-time quantitative PCR revealed elevated steady-state transcript levels in the eggs, miracidia and paired adult worms compared to other stages. In parallel with gene expression profiles, an affinity-purified anti-SmPA28γ antibody produced against recombinant protein exhibited strongest reactivity in Western blot analyses to endogenous SmPA28γ from miracidia, sporocysts and paired adult worms. Given its known regulatory function in other organisms, we hypothesized that the high level of SmPA28γ transcript and protein in these stages may be correlated with an important role of the PA28γ in the cellular growth and/or development of this parasite. To address this hypothesis, miracidia were transformed in vitro to sporocysts in the presence of SmPA28γ double-stranded RNAs (dsRNAs) and cultivated for 4 days, after which time steady-state transcript and protein levels, and phenotypic changes were evaluated. SmPA28γ dsRNA treatment resulted in gene and protein knockdown of ~60% and ~80%, respectively, which were correlated with a significant decrease in larval length compared to its controls. These findings are consistent with a putative role of SmPA28γ in larval growth/development of the S. mansoni.

Spatial arrangement and functional role of α subunits of proteasome activator PA28 in hetero-oligomeric form

A major form of proteasome activator PA28 is a heteroheptamer composed of interferon-γ-inducible α and β subunits, which share approximately 50% amino acid identity and possess distinct insert loops. This activator forms a complex with the 20S proteasome and thereby stimulates proteasomal degradation of peptides in an ATP-independent manner, giving rise to smaller antigenic peptides presented by major histocompatibility complex class I molecules. In this study, we performed biophysical and biochemical characterization of the structure and function of the PA28 hetero-oligomer. Deuteration-assisted small-angle neutron scattering demonstrated three α and four β subunits are alternately arranged in the heptameric ring. In this arrangement, PA28 loops surround the central pore of the heptameric ring (site for peptide entry). Activating the 20S proteasome with a PA28 mutant that lacked the α subunit loops cleaved model substrates longer than a nonapeptide with better efficiency when compared to wild-type PA28. Based on these data, we hypothesize that the flexible PA28 loops act as gatekeepers, which function to select the length of peptide substrates to be transported between the proteolytic chamber and the extra-proteasomal medium.

The Ubiquitin-Proteasome System in Huntington's Disease: Are Proteasomes Impaired, Initiators of Disease, or Coming to the Rescue?

Huntington's disease is a progressive neurodegenerative disease, caused by a polyglutamine expansion in the huntingtin protein. A prominent hallmark of the disease is the presence of intracellular aggregates initiated by N-terminal huntingtin fragments containing the polyglutamine repeat, which recruit components of the ubiquitin-proteasome system. While it is commonly thought that proteasomes are irreversibly sequestered into these aggregates leading to impairment of the ubiquitin-proteasome system, the data on proteasomal impairment in Huntington's disease is contradictory. In addition, it has been suggested that proteasomes are unable to actually cleave polyglutamine sequences in vitro, thereby releasing aggregation-prone polyglutamine peptides in cells. Here, we discuss how the proteasome is involved in the various stages of polyglutamine aggregation in Huntington's disease, and how alterations in activity may improve clearance of mutant huntingtin fragments.

Assembly and function of the proteasome

Proteasome is a highly organized protease complex comprising a catalytic 20S core particle (CP) and two 19S regulatory particles (RP), which together form the 26S structure. The 26S proteasome is responsible for the degradation of most ubiquitylated proteins through a multistep process involving recognition of the polyubiquitin chain, unfolding of the substrate, and translocation of the substrate into the active site in the cavity of the CP. Recent studies have shed light on various aspects of the complex functions of the 26S proteasome. In addition, the recent identification of various proteasome-dedicated chaperones indicates that the assembly pathways of the RP and CP are multistep processes. In this review, we summarize recent advances in the understanding of the proteasome structure, function, and assembly.

Structure of the proteasome

The ubiquitin-proteasomal system is an essential element of the protein quality control machinery in cells. The central part of this system is the 20S proteasome. The proteasome is a barrel-shaped multienzyme complex, containing several active centers hidden at the inner surface of the hollow cylinder. So, the regulation of the substrate entry toward the inner proteasomal surface is a key control mechanism of the activity of this protease. This chapter outlines the knowledge on the structure of the subunits of the 20S proteasome, the binding and structure of some proteasomal regulators and inducible proteasomal subunits. Therefore, this chapter imparts the knowledge on proteasomal structure which is required for the understanding of the following chapters.

REG-γ associates with and modulates the abundance of nuclear activation-induced deaminase

REG-γ, a protein involved in protein degradation, binds to nuclear AID, and REG-γ–deficient B cells contain more AID and exhibit increased immunoglobulin class switching.

Activation-induced deaminase (AID) acts on the immunoglobulin loci in activated B lymphocytes to initiate antibody gene diversification. The abundance of AID in the nucleus appears tightly regulated, with most nuclear AID being either degraded or exported back to the cytoplasm. To gain insight into the mechanisms regulating nuclear AID, we screened for proteins interacting specifically with it. We found that REG-γ, a protein implicated in ubiquitin- and ATP-independent protein degradation, interacts in high stoichiometry with overexpressed nuclear AID as well as with endogenous AID in B cells. REG-γ deficiency results in increased AID accumulation and increased immunoglobulin class switching. A stable stoichiometric AID–REG-γ complex can be recapitulated in co-transformed bacteria, and REG-γ accelerates proteasomal degradation of AID in in vitro assays. Thus, REG-γ interacts, likely directly, with nuclear AID and modulates the abundance of this antibody-diversifying but potentially oncogenic enzyme.

The immunoproteasomes regulate LPS-induced TRIF/TRAM signaling pathway in murine macrophages

We have proposed the novel concept that the macrophage ubiquitin-proteasome pathway functions as a key regulator of Lipopolysaccharide (LPS)-induced inflammation signaling. These findings suggest that proteasome-associated protease subunits X, Y, and Z are replaced by LMP subunits after LPS treatment of RAW 264.7 cells. The objective here was to determine the contribution of selective LMP proteasomal subunits to LPS-induced nitric oxide (NO) and TNF-α production in primary murine macrophages. Accordingly, thioglycollate-elicited macrophages from LMP7, LMP2, LMP10 (MECL-1), and LMP7/MECL-1 double knockout mice were stimulated in vitro with LPS, and were found to generate markedly reduced NO levels compared to wild-type (WT) mice, whereas TNF-α levels responses were essentially unaltered relative to wild-type responses. The recent studies suggest that the TRIF/TRAM pathway is defective in LMP knockouts which may explain why iNOS/NO are not robustly induced in LPS-treated macrophages from knockouts. Treating these macrophages with IFN-γ and LPS, however, reverses this defect, leading to robust NO induction. TNF-α is induced by LPS in the LMP knockout macrophages because IκB and IRAK are degraded normally via the MyD88 pathway. Collectively, these findings strongly support the concept that LMP7/MECL-1 proteasomes subunits actively function to regulate LPS-induced NO production by affecting the TRIF/TRAM pathway.

LPS-induced formation of immunoproteasomes: TNF-α and nitric oxide production are regulated by altered composition of proteasome-active sites

Stimulation of mouse macrophages with LPS leads to tumor necrosis factor (TNF-α) secretion and nitric oxide (NO) release at different times through independent signaling pathways. While the precise regulatory mechanisms responsible for these distinct phenotypic responses have not been fully delineated, results of our recent studies strongly implicate the cellular cytoplasmic ubiquitin-proteasome pathway as a key regulator of LPS-induced macrophage inflammatory responses. Our objective in this study was to define the relative contribution of specific proteasomal active-sites in induction of TNF-α and NO after LPS treatment of RAW 264.7 macrophages using selective inhibitors of these active sites. Our data provide evidence that LPS stimulation of mouse macrophages triggers a selective increase in the levels of gene and protein expression of the immunoproteasomes, resulting in a modulation of specific functional activities of the proteasome and a corresponding increase in NO production as compared to untreated controls. These findings suggest the LPS-dependent induction of immunoproteasome. In contrast, we also demonstrate that TNF-α expression is primarily dependent on both the chymotrypsin- and the trypsin-like activities of X, Y, Z subunits of the proteasome. Proteasome-associated post-acidic activity alone also contributes to LPS-induced expression of TNF-α. Taken together; our results indicate that LPS-induced TNF-α in macrophages is differentially regulated by each of the three proteasome activities. Since addition of proteasome inhibitors to mouse macrophages profoundly affects the degradation of proteins involved in signal transduction, we conclude that proteasome-specific degradation of several signaling proteins is likely involved in differential regulation of LPS-dependent secretion of proinflammatory mediators.

Epstein-Barr virus lytic cycle activation alters proteasome subunit expression in Burkitt's lymphoma cells

We have shown that Epstein-Barr virus (EBV) lytic cycle activation in Burkitt's lymphoma (BL) cells down-regulates chymotrypsin- and caspase-like activities of the proteasome. The aim of the present study was to evaluate whether EBV activation might also affect proteasome subunit composition. Our results indicate that, independently of the latency program established in the host cells, induction of the EBV lytic cycle reduces the expression of the proteasomal components β5, β1 and β2i, whereas it increases that of β2, β1i, PA28α and PA28β. The modulation of the composition and enzymatic activities of the proteolytic complex are indicative of a less efficient generation of viral immunoepitopes.

Emerging roles of the 26S proteasome in nuclear hormone receptor-regulated transcription

The mechanisms by which nuclear hormone receptors (NHRs) regulate transcription are highly dynamic and require interplay between a myriad of regulatory protein complexes including the 26S proteasome. Protein degradation is the most well-established role of the proteasome; however, an increasing body of evidence suggests that the 26S proteasome may regulate transcription in proteolytic and nonproteolytic mechanisms. Here we review how these mechanisms may apply to NHR-mediated transcriptional regulation. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!

Functional alterations of cardiac proteasomes under physiological and pathological conditions

The cardiac proteasome is a complex, heterogeneous, and dynamic organelle. Its function is regulated by its molecular organization, post-translational modifications, and associated partner proteins. Pressure overload, ischaemic heart disease, or genetic mutations in contractile proteins can cause heart failure, during which misfolded protein levels are elevated. At the same time, numerous interconnected signal transduction pathways are activated that may modulate any of the three proteasomal regulatory mechanisms mentioned above, resulting in functional changes in cardiac proteasomes. Many lines of evidence support the important role of the ubiquitin-proteasome system (UPS) in the development of heart diseases. Many researchers have focused on the UPS, applying new drug discovery methods not only in the field of cancer research but also in cardiovascular fields such as cardiac hypertrophy and ischaemic heart diseases. More understanding of UPS in the pathophysiology of heart diseases will lead to new routes for therapy.

Proteasome inhibitors and cardiac cell growth

Activation of the ubiquitin-proteasome system has been described in different models of cardiac hypertrophy. Cardiac cell growth in response to pressure or volume overload, as well as physiological adaptive hypertrophy, is accompanied by an increase in protein ubiquitination, proteasome subunit expression, and proteasome activity. Importantly, an inhibition of proteasome activity prevents and reverses cardiac hypertrophy and remodelling in vivo. The focus of this review is to provide an update about the mechanisms by which proteasome inhibitors affect cardiac cell growth in adaptive and maladaptive models of cardiac hypertrophy. In the first part, we summarize how the proteasome affects both proteolysis and protein synthesis in a context of cardiac cell growth. In the second part, we show how proteasome inhibition can prevent and reverse cardiac hypertrophy and remodelling in response to different conditions of overload.

Protein degradation systems in viral myocarditis leading to dilated cardiomyopathy

The primary intracellular protein degradation systems, including the ubiquitin-proteasome and the lysosome pathways, have been emerging as central regulators of viral infectivity, inflammation, and viral pathogenicity. Viral myocarditis is an inflammatory disease of the myocardium caused by virus infection in the heart. The disease progression of viral myocarditis occurs in three distinct stages: acute viral infection, immune cell infiltration, and cardiac remodelling. Growing evidence suggests a crucial role for host proteolytic machineries in the regulation of the pathogenesis and progression of viral myocarditis in all three stages. Cardiotropic viruses evolve different strategies to subvert host protein degradation systems to achieve successful viral replication. In addition, these proteolytic systems play important roles in the activation of innate and adaptive immune responses during viral infection. Recent evidence also suggests a key role for the ubiquitin-proteasome and lysosome systems as the primary effectors of protein quality control in the regulation of cardiac remodelling. This review summarizes the recent advances in understanding the direct interaction between cardiotropic viruses and host proteolytic systems, with an emphasis on coxsackievirus B3, one of the primary aetiological agents causing viral myocarditis, and highlights possible roles of the host degradation systems in the pathogenesis of viral myocarditis and its progression to dilated cardiomyopathy.

The tumor proteasome as a novel target for gold(III) complexes: implications for breast cancer therapy

Although cisplatin plays a vital role in the treatment of several types of human cancer, its wide use is limited by the development of drug resistance and associated toxic side effects. Gold and gold complexes have been used to treat a wide range of ailments for many centuries. In recent years, the use of gold(III) complexes as an alternative to cisplatin treatment was proposed due to the similarities of gold and platinum. Gold(III) is isoelectronic with platinum(II) and gold(III) complexes have the same square-planar geometries as platinum(II) complexes, such as cisplatin. Although it was originally thought that gold(III) complexes might have the same molecular target as cisplatin, several lines of data indicated that proteins, rather than DNA, are targeted by gold complexes. We have recently evaluated cytotoxic and anti-cancer effects of several gold(III) dithiocarbamates against human breast cancer cells in vitro and in vivo. We have identified the tumor proteasome as an important target for gold(III) complexes and have shown that proteasome inhibition by gold(III) complexes is associated with apoptosis induction in breast cancer cells in vitro and in vivo. Furthermore, treatment of human breast tumor-bearing nude mice with a gold(III) dithiocarbamate complex was associated with tumor growth inhibition, supporting the significance of its potential development for breast cancer treatment.

The proteasome: overview of structure and functions

The proteasome is a highly sophisticated protease complex designed to carry out selective, efficient and processive hydrolysis of client proteins. It is known to collaborate with ubiquitin, which polymerizes to form a marker for regulated proteolysis in eukaryotic cells. The highly organized proteasome plays a prominent role in the control of a diverse array of basic cellular activities by rapidly and unidirectionally catalyzing biological reactions. Studies of the proteasome during the past quarter of a century have provided profound insights into its structure and functions, which has appreciably contributed to our understanding of cellular life. Many questions, however, remain to be elucidated.

Allele-selective effect of PA28 in MHC class I antigen processing

PA28 is an IFN-gamma-inducible proteasome activator and its genetic ablation causes complete loss of processing of certain Ags, but not all of them. The reason why this occurs and how PA28 influences the formation of peptide repertoires for MHC class I molecules remains unknown. In this study, we show the allele-specific role of PA28 in Ag processing. Retrovirus-transduced overexpression of PA28alpha decreased expression of K(d) (D(d)) while it increased K(b) and L(d) on the cell surface. By contrast, overexpression of PA28alphaDeltaC5, a mutant carrying a deletion of its five C-terminal residues and capable of attenuating the activity of endogenous PA28, produced the opposite effect on expression of those MHC class I molecules. Moreover, knockdown of both PA28alpha and beta by small-interfering RNA profoundly augmented expression of K(d) and D(d), but not of L(d), on the cell surface. Finally, we found that PA28-associated proteasome preferentially digested within epitopic sequences of K(d), although correct C-terminal flankings were removed, which in turn hampered production of K(d) ligands. Our results indicate that whereas PA28 negatively influences processing of K(d) (D(d)) ligands, thereby, down-regulating Ag presentation by those MHC class I molecules, it also efficiently produces K(b) (L(d)) epitopes, leading to up-regulation of the MHC molecules.

Role of proteasomes in cellular regulation

The 26S proteasome is the key enzyme of the ubiquitin-dependent pathway of protein degradation. This energy-dependent nanomachine is composed of a 20S catalytic core and associated regulatory complexes. The eukaryotic 20S proteasomes demonstrate besides several kinds of peptidase activities, the endoribonuclease, protein-chaperone and DNA-helicase activities. Ubiquitin-proteasome pathway controls the levels of the key regulatory proteins in the cell and thus is essential for life and is involved in regulation of crucial cellular processes. Proteasome population in the cell is structurally and functionally heterogeneous. These complexes are subjected to tightly organized regulation, particularly, to a variety of posttranslational modifications. In this review we will summarize the current state of knowledge regarding proteasome participation in the control of cell cycle, apoptosis, differentiation, modulation of immune responses, reprogramming of these particles during these processes, their heterogeneity and involvement in the main levels of gene expression.

A tale of two giant proteases

The 26S proteasome and tripeptidyl peptidase II (TPPII) are two exceptionally large eukaryotic protein complexes involved in intracellular proteolysis, where they exert their function sequentially: the proteasome, a multisubunit complex of 2.5 MDa, acts at the downstream end of the ubiquitin pathway and degrades ubiquitinylated proteins into small oligopeptides. Such oligopeptides are substrates for TPPII, a 6-MDa homooligomer, which releases tripeptides from their free N-terminus. Both 26S and TPPII are very fragile complexes refractory to crystallization and in their fully assembled native form have been visualized only by electron microscopy. Here, we will discuss the structural features of the two complexes and their functional implications.

Implication of altered proteasome function in alcoholic liver injury

The proteasome is a major protein-degrading enzyme, which catalyzes degradation of oxidized and aged proteins, signal transduction factors and cleaves peptides for antigen presentation. Proteasome exists in the equilibrium of 26S and 20S particles. Proteasome function is altered by ethanol metabolism, depending on oxidative stress levels: low oxidative stress induces proteasome activity, while high oxidative stress reduces it. The proposed mechanisms for modulation of proteasome activity are related to oxidative modification of proteasomal proteins with primary and secondary products derived from ethanol oxidation. Decreased proteolysis by the proteasome results in the accumulation of insoluble protein aggregates, which cannot be degraded by proteasome and which further inhibit proteasome function. Mallory bodies, a common signature of alcoholic liver diseases, are formed by liver cells, when proteasome is unable to remove cytokeratins. Proteasome inhibition by ethanol also promotes the accumulation of pro-apoptotic factors in mitochondria of ethanol-metabolizing liver cells that are normally degraded by proteasome. In addition, decreased proteasome function also induces accumulation of the negative regulators of cytokine signaling (I-κB and SOCS), thereby blocking cytokine signal transduction. Finally, ethanol-elicited blockade of interferon type 1 and 2 signaling and decreased proteasome function impairs generation of peptides for MHC class I-restricted antigen presentation.

Upregulation of a Small Subset of Genes Drives Type I Interferon-Induced Antiviral Memory

Interferons (IFNs) stand in the frontline of defense against viral infections. In this study, we aimed at characterizing the gene expression profile specific to the antiviral effect out of the hundreds of genes involved also in other IFN activities. We found that the IFN-induced antiviral state is maintained for a prolonged time even after IFN occlusion. This was achieved through the active expression of a small set of <40 genes long after IFN was occluded, from which two groups are distinguished: one includes genes participating in direct inhibition of viral replication, such as Mx and OAS; the second group is related to antigen presentation, including all genes involved in the proteasome-to-immunoproteasome switch and class I MHC genes. Transcription of these genes continued after IFN removal and was Stat1 independent, suggesting the involvement of other signaling elements in addition to the canonical signal transduction pathway. Not less important were genes whose upregulation, in cases by many fold, is terminated once IFN is removed. Among these are viral sensing genes, such as retinoic acid-inducible gene-I protein (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and toll-like receptor (TLR), cytokines, and apoptotic-related genes. Our findings provide a systemwide depiction of prolonged intracellular antiviral protection without the need for ongoing IFN stimulation.

Proteasomes: machines for all reasons

Emerging data reveal that besides degrading proteins tagged with ubiquitin, the proteasome plays a more varied and decisive role in cellular regulation than previously imagined. In this issue, Hanna et al. (2007) expand our view of the proteasome by showing that under certain conditions, proteasome composition can be altered to control ubiquitin homeostasis.

Molecular cloning of proteasome activator PA28-beta subunit of large yellow croaker (Pseudosciana crocea) and its coordinated up-regulation with MHC class I alpha-chain and beta 2-microglobulin in poly I:C-treated fish

Antigenic peptides presented on MHC class I molecules to cytotoxic T-cells are generated in the cytosol by the 20S proteasome. Two activators PA28-alpha and PA28-beta, which are inducible by interferon-gamma (IFN-gamma), activate the latent 20S proteasome, thus playing an important role in the processing of MHC class I antigen. Molecular properties and function in the MHC class I antigen processing of PA28 have been well studied and documented in mammals while little is known in fish. In the present study, we reported the cloning of a PA28-beta gene homologue from the spleen of large yellow croaker (Pseudosciana crocea), an economically important marine fish (LycPA28-beta). The full-length cDNA of LycPA28-beta is 1133 nucleotides (nt) encoding a protein of 245 amino acids (aa), with a putative molecular weight of 27.7 kDa. The deduced protein shares 76, 69, 61, 60, 59, 57 and 57% sequence identity to sequences found in zebrafish, flounder, pig, rat, mouse, cattle and human, respectively. The deduced LycPA28-beta contains a PA28-beta subunit-specific insert in the region corresponding to the KEKE motif of the known PA28-alpha (Region B), a conserved activation loop (Region C) and a highly homologous C-terminal region among all three PA28 subunits (Region E), and a characteristic proline-rich motif (Region A) and a potential protein kinase C recognition site (Region D). Western blot analysis of various tissues indicated that LycPA28-beta was constitutively expressed in kidney, liver, spleen and intestine, and weakly expressed in muscle tissue, but not detected in gills, heart and brain. The LycPA28-beta expression was significantly up-regulated in kidney, liver, spleen, intestine and muscle tissues, and also induced in gills after 72 h of treatment with a viral micmic, polyinosinic polycytidynic acid (poly I:C). The transcriptional analysis of LycPA28-beta and MHC class I alpha-chain (alpha-chain) and beta(2)-microglobulin (beta(2)m) in spleens of poly I:C-induced large yellow croaker was further performed by RT-PCR. The results showed that the expression of LycPA28-beta and class I alpha-chain and beta(2)m genes was coordinately up-regulated by poly I:C, suggesting that induction of the MHC class I antigen processing and presentation pathway may be required for the antiviral immune response triggered poly I:C in large yellow croaker.

MPTP treatment of common marmosets impairs proteasomal enzyme activity and decreases expression of structural and regulatory elements of the 26S proteasome

Dysfunction of the ubiquitin-proteasome system occurs in the substantia nigra (SN) in Parkinson's disease (PD). However, it is unknown whether this is a primary cause or a secondary consequence of other components of the pathogenic process. We have investigated in nonhuman primates whether initiating cell death through mitochondrial complex I inhibition using 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride (MPTP) altered proteasomal activity or the proteasomal components in the SN. Chymotrypsin-like, trypsin-like and peptidylglutamyl-peptide hydrolase (PGPH) activating of 20S proteasome were decreased in SN homogenates of MPTP-treated marmosets compared to naïve animals. Western blotting revealed a marked decrease in the expression of 20S-alpha subunits, but no change in 20S-beta subunits in the SN of MPTP-treated marmoset compared to naïve animals. There was a marked decrease in the expression of the proteasome activator 700 (PA700) and proteasome activator 28 (PA28) regulatory complexes. The 20S-alpha4 subunit immunoreactivity was decreased in the nucleus of colocalized tyrosine hydroxylase (TH)-positive cells of MPTP-treated animals compared to naïve animals but no difference in the intensity of 20S-beta1i subunit staining. Immunoreactivity for PA700-Rpt5 and PA28-alpha subunits within surviving TH-positive cells of MPTP-treated marmoset was reduced compared to naïve controls. Overall, the changes in proteasomal function and structure occurring follow MPTP-induced destruction of the SN in common marmosets were very similar to those found in PD. This suggests that altered proteasomal function in PD could be a consequence of other pathogenic processes occurring in SN as opposed to initiating cell death as previously suggested.

The involvement of immunoproteasomes in induction of MHC class I-restricted immunity targeting Toxoplasma SAG1

The ubiquitin-proteasome system (UPS) plays an indispensable role in inducing MHC class I-restricted CD8+ T cells and was exploited in the development of a DNA vaccine against the intracellular protozoan Toxoplasma gondii by constructing a chimeric DNA encoding a fusion protein between murine ubiquitin and the toxoplasma antigen SAG1. The SAG1 peptide was promptly degraded in antigen-presenting cells (APCs) transfected with the chimeric DNA. Degradation, however, was hampered by incubating the APCs with the proteasome inhibitor epoxomicin. Mice vaccinated with the DNA acquired potent protective immunity mediated by MHC class I-restricted CD8+ T cells against infection by the highly virulent Toxoplasma. The accelerated degradation and induction of immunity were dependent on the UPS since mice lacking an immuno-subunit of 20S proteasome, LMP7, lost these functions, although they were independent of the proteasome regulator PA28alpha/beta complex.

Immuno-proteasome subunit LMP7 is up-regulated in the ischemic kidney in an experimental model of renovascular hypertension

Immuno-proteasome is thought to be responsible for the processing of intracellular antigens and is induced when cells are treated with the inflammatory cytokines promoting cellular immunity. We tested the possibility that immuno-proteasome can be up-regulated in renal cells exposed to a long-lasting ischemia and inflammation in an experimental model of two-kidney, one-clip renovascular hypertension in the rat. Western blotting showed that immuno-proteasome subunit, LMP7, was up-regulated in the clipped ischemic kidney that was atrophic, but not in the contralateral unclipped kidney that underwent compensatory hypertrophy. Immunohistochemical analysis revealed that LMP7 was highly expressed in cortical epithelial and endothelial cells of the ischemic kidney. Surprisingly, the second immuno-subunit, LMP2, was almost undetectable, indicating that renal ischemia may induce exclusively the LMP7 subunit. We also found that renal ischemia neither reduced the SDS-stimulated proteasomal activity nor affected a high level of the PA28 activator. Thus, the results provide evidence that LMP7 immuno-subunit is induced in renal cells exposed to a long-lasting renal ischemia and inflammation, and that there is a direct link between LMP induction and renal atrophy. This opens an opportunity to study a role for LMP-containing proteasomes in the kidneys and other organs undergoing reduction in mass in diseases accompanied by a long-lasting ischemia and inflammatory responses.

Redox modulation of cellular metabolism through targeted degradation of signaling proteins by the proteasome

Under conditions of oxidative stress, the 20S proteasome plays a critical role in maintaining cellular homeostasis through the selective degradation of oxidized and damaged proteins. This adaptive stress response is distinct from ubiquitin-dependent pathways in that oxidized proteins are recognized and degraded in an ATP-independent mechanism, which can involve the molecular chaperone Hsp90. Like the regulatory complexes 19S and 11S REG, Hsp90 tightly associates with the 20S proteasome to mediate the recognition of aberrant proteins for degradation. In the case of the calcium signaling protein calmodulin, proteasomal degradation results from the oxidation of a single surface exposed methionine (i.e., Met145); oxidation of the other eight methionines has a minimal effect on the recognition and degradation of calmodulin by the proteasome. Since cellular concentrations of calmodulin are limiting, the targeted degradation of this critical signaling protein under conditions of oxidative stress will result in the downregulation of cellular metabolism, serving as a feedback regulation to diminish the generation of reactive oxygen species. The targeted degradation of critical signaling proteins, such as calmodulin, can function as sensors of oxidative stress to downregulate global rates of metabolism and enhance cellular survival.

Purification and assay of proteasome activator PA200

PA200, the most recently discovered activator of the 20S proteasome, is a nuclear protein thought to play a role in DNA repair. Homologs of PA200 have been found in rat, frog, birds, worms, and budding yeast, where it is called Blm3p (now known as Blm10p), but not in Drosophila or fission yeast. Western blots of SDS-PAGE transfers reveal 160 and 200K forms of mammalian PA200, and organ surveys demonstrate that the 200K species is highest in testis. PA200 purified from bovine testis binds the ends of the cylindrical 20S proteasome, forming volcano-shaped structures in negatively stained EM images. In vitro assays demonstrate that binding of PA200 activates peptide hydrolysis by the 20S proteasome. This chapter describes the purification and assay of bovine testis PA200.

Mobilizing the proteolytic machine: cell biological roles of proteasome activators and inhibitors

Proteasomes perform the majority of proteolysis that occurs in the cytosol and nucleus of eukaryotic cells and, thereby, perform crucial roles in cellular regulation and homeostasis. Isolated proteasomes are inactive because substrates cannot access the proteolytic sites. PA28 and PA200 are activators that bind to proteasomes and stimulate the hydrolysis of peptides. Several protein inhibitors of the proteasome have also been identified, and the properties of these activators and inhibitors have been characterized biochemically. By contrast, their physiological roles--which have been reported to include production of antigenic peptides, proteasome assembly and DNA repair--are controversial. In this article, we briefly review the biochemical data and discuss the possible biological roles of PA28, PA200 and proteasome inhibitors.

The axial channel of the 20S proteasome opens upon binding of the PA200 activator

Proteasomes consist of a proteolytic core called the 20 S particle and ancillary factors that regulate its activity in various ways. PA200 has been identified as a large (200 kDa) nuclear protein that stimulates proteasomal hydrolysis of peptides. To characterize its interaction with the 20 S core, we have visualized PA200-20 S complexes by electron microscopy. Monomers of PA200 bind to one or both ends of the 20 S core. Reconstructed in three dimensions to 23 A resolution from cryo-electron micrographs of the singly bound complex, PA200 has an asymmetric dome-like structure with major and minor lobes. Taking into account previous bioinformatic analysis, it is likely to represent an irregular folding of an alpha-helical solenoid composed of HEAT-like repeats. PA200 makes contact with all alpha-subunits except alpha7, and this interaction induces an opening of the axial channel through the alpha-ring. Thus, the activation mechanism of PA200 is expressed via its allosteric effects on the 20 S core particle, perhaps facilitating release of digestion products or the entrance of substrates.

Preparation of hybrid (19S-20S-PA28) proteasome complexes and analysis of peptides generated during protein degradation

PA28 (also named REG or 11S) is a ring-shaped (180-kDa) interferon-gamma-induced complex that associates with the 20S proteasome and dramatically stimulates the breakdown of short peptides. Immunoprecipitation studies indicate that in vivo PA28 also exists in larger complexes that also contain the 19S particle, which is required for the ATP-ubiquitin-dependent degradation of proteins. However, because of its lability (e.g., it does not withstand exposure to high ionic strength buffers), this larger complex cannot be purified by standard biochemical protocols. Therefore, we developed a method to reconstitute in vitro such hybrid proteasomes (i.e., PA28-20S-19S) from highly purified components. This chapter describes conditions that allow the association of PA28 with "singly capped" 26S (i.e., 19S-20S) particles. In addition assays are described to measure absolute rates of degradation of several non-ubiquitinated proteins by 26S and 20S proteasomes and methods to analyze the pattern and size distribution of peptides generated during the degradation of these proteins.

Purification and Analysis of Recombinant 11S Activators of the 20S Proteasome: Trypanosoma brucei PA26 and Human PA28α, PA28β, and PA28γ

Proteasomes perform the bulk of nonlysosomal degradation of aberrant, damaged, misfolded, and naturally short-lived regulatory proteins in eukaryotic cells. They are approximately 700-kDa assemblies whose hollow architecture sequesters the proteolytic sites inside a central chamber, thereby ensuring that the activity of isolated proteasomes is repressed. In vivo, proteasomes are activated by protein complexes, including the 11S activators (PA28 and PA26), which bind to one or both ends of the barrel-shaped structure. This chapter describes protocols for the purification of recombinant 11S regulators, characterization of their ability to stimulate proteasome activity, and crystallization of proteasome complexes.

The Use of Mass Spectrometry to Identify Antigens from Proteasome Processing

Mass spectrometry (MS) is a powerful tool for the characterization of antigenic peptides that play a major role in the immune system. Most of the major histocompatibility complex (MHC) class I peptides are generated during the degradation of intracellular proteins by the proteasome, a catalytic complex present in all eukaryotic cells. This chapter focuses on the contribution of MS to the understanding of the mechanisms of antigen processing by the proteasome. This knowledge may be valuable for the design of specific inhibitors of proteasome, which has recently been recognized as a therapeutic target in cancer therapies and for the development of efficient peptidic vaccines in immunotherapies. Examples from the literature have been chosen to illustrate how MS data can contribute first to the understanding of the mechanisms of proteasomal processing and, second, to the understanding of the crucial role of proteasome in cytotoxic T lymphocytes (CTL) activation. The general strategy based on MS analyses used in these studies is also described.

New HEAT-like repeat motifs in proteins regulating proteasome structure and function

We have identified repeat motifs in the large proteasome-binding proteins PA200 and Ecm29 by applying a sensitive sequence profile method. These repeat motifs, especially those of PA200, resemble HEAT/ARM repeats in length and other properties but differ from them in the occupancy of certain positions. The HEAT motif consists of two alpha-helices and two turns: molecular modeling suggests that in the PA200 and Ecm29 repeats, the alpha-helices may be slightly turned relative to their orientations in typical HEAT repeats. Both PA200 and Ecm29 are composed almost entirely of such repeats, and therefore are likely to have alpha-helical solenoid structures. These observations lead us to speculate on how PA200 and Ecm29 may associate with proteasomes.

Conformational and enzymatic changes of 20S proteasome of rat natural killer cells induced by mono- and divalent cations

We have been investigated the relation between activation of "neutral" and "acidic" chymotrypsin-like (ChT-L) activity and conformational changes in the 20S proteasome complex from the rat natural killer (NK) cells induced by SDS, mono- and divalent cations. The conformational changes were monitored by tryptophan fluorescence and light scattering. It was revealed that the changes in the maximum position and contribution of the short-wavelength spectral component correlated with the alteration of ChT-L activity of the proteasome. Statistical analysis was applied to assign the fluorescence components with tryptophan residues based on the classification of calculated structural parameters of the environment of tryptophan fluorophores in protein. It was proposed that the emission of W13 from alpha6-subunit located near the cluster of highly conserved proteasome residues is mostly sensitive to the activation of the enzyme. We concluded that the expression of maximal ChT-L activity of 20S proteasome is associated with the conformational changes occurs in this cluster that lead to the proteasome open conformation, allowing substrate access into the proteolytic chamber.

Archaeal proteasomes: potential in metabolic engineering

Archaea are a valuable source of enzymes for industrial and scientific applications because of their ability to survive extreme conditions including high salt and temperature. Thanks to advances in molecular biology and genetics, archaea are also attractive hosts for metabolic engineering. Understanding how energy-dependent proteases and chaperones function to maintain protein quality control is key to high-level synthesis of recombinant products. In archaea, proteasomes are central players in energy-dependent proteolysis and form elaborate nanocompartments that degrade proteins into oligopeptides by processive hydrolysis. The catalytic core responsible for this proteolytic activity is the 20S proteasome, a barrel-shaped particle with a central channel and axial gates on each end that limit substrate access to a central proteolytic chamber. AAA proteins (ATPases associated with various cellular activities) are likely to play several roles in mediating energy-dependent proteolysis by the proteasome. These include ATP binding/hydrolysis, substrate binding/unfolding, opening of the axial gates, and translocation of substrate into the proteolytic chamber.

Substrate access and processing by the 20S proteasome core particle

Intracellular proteolysis is an essential process. In eukaryotes, most proteins in the cytosol and nucleus are degraded by the ubiquitin (Ub)-proteasome pathway. A major component within this system is the 26S proteasome, a 2.5MDa molecular machine, built from more than 31 different subunits. This complex is formed by a cylinder-shaped multimeric complex referred to as the proteolytic 20S proteasome (core particle, CP) capped at each end by another multimeric component called the 19S complex (regulatory particle, RP) or PA700. Structure, assembly and enzymatic mechanism have been elucidated only for the CP, whereas the organization of the RP is less well understood. The CP is composed of 28 subunits, which are arranged as an alpha7beta7beta7alpha7-complex in four stacked rings. The interior of the free core particle, which harbors the active sites, is inaccessible for folded and unfolded substrates and represents a latent state. This inhibition is relieved upon binding of the RP to the CP by formation of the 26S proteasome holoenzyme. This review summarizes the current knowledge of the structural features of 20S proteasomes.

Are Huntington's and polyglutamine-based ataxias proteasome storage diseases?

To date, 10 neurological diseases, including Huntington's and several ataxias, are caused by a lengthening of glutamine (Q) tracts in various proteins. Even though the Q expansions arise in unrelated proteins, the diseases share three striking features: (1) 35 contiguous glutamines constitutes the pathological threshold for 9 of the 10 diseases; (2) the Q-expanded proteins are expressed in many tissues, yet pathology is largely restricted to neurons; and (3) the Q-expanded proteins or fragments thereof form nuclear inclusions that also contain ubiquitin, proteasomes and chaperones. Our studies of the proteasome activator REGgamma suggest a possible explanation for these shared properties. REGgamma is highly expressed in brain, located in the nucleus and actually suppresses the proteasome active sites principally responsible for cleaving glutamine-MCA bonds. These observations coupled with reports that peptides longer than 35 residues, the polyQ pathology threshold, are unable to diffuse out of the proteasome suggest the following hypothesis. Proteins containing long glutamine tracts are efficiently pumped into REGgamma-capped 26S proteasomes, but REGgamma suppression of cleavage after glutamine produces polyQ fragments too long to diffuse out of the 20S proteolytic core thereby inactivating the 26S proteasome. In effect, we hypothesize that the polyQ pathologies may be proteasomal storage diseases analogous to disorders of lysosome catabolism.

Differential expression of ubiquitin and proteasome-dependent pathway components in rat tissues

The ATP-ubiquitin-dependent pathway in eukaryotes is a complex system, which plays an essential role in selective protein degradation. The functional diversity of this system must be matched to the specific protein metabolism related to the physiology of each cell types. The aim of our work was to study the expression of different components of the proteasome-dependent pathway in various rat tissues. Therefore we quantified the 20S proteasome and the 19S and 11S regulators by Western blot, and measured the expression of the mRNAs of certain subunits, which are markers of these components. We compared the peptidase activities of the purified 20S proteasomes, and also mapped its components by 2D electrophoresis. Our results show that the components of the ATP-ubiquitin-dependent pathway vary considerably both in abundance and activity from one tissue to another. This diversity allows the cells to respond appropriately to tissue-specific protein metabolism in the rat.