19S Cap Research Articles

Proteostatic Remodeling of Small Heat Shock Chaperones─Crystallins by Ran-Binding Protein 2─and the Peptidyl-Prolyl cis-trans Isomerase and Chaperone Activities of Its Cyclophilin Domain.

Disturbances in protein phase transitions promote protein aggregation─a neurodegeneration hallmark. The modular Ran-binding protein 2 (Ranbp2) is a cytosolic molecular hub for rate-limiting steps of phase transitions of Ran-GTP-bound protein ensembles exiting nuclear pores. Chaperones also regulate phase transitions and proteostasis by suppressing protein aggregation. Ranbp2 haploinsufficiency promotes the age-dependent neuroprotection of the chorioretina against phototoxicity by proteostatic regulations of neuroprotective substrates of Ranbp2 and by suppressing the buildup of polyubiquitylated substrates. Losses of peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone activities of the cyclophilin domain (CY) of Ranbp2 recapitulate molecular effects of Ranbp2 haploinsufficiency. These CY impairments also stimulate deubiquitylation activities and phase transitions of 19S cap subunits of the 26S proteasome that associates with Ranbp2. However, links between CY moonlighting activity, substrate ubiquitylation, and proteostasis remain incomplete. Here, we reveal the Ranbp2 regulation of small heat shock chaperones─crystallins in the chorioretina by proteomics of mice with total or selective modular deficits of Ranbp2. Specifically, loss of CY PPIase of Ranbp2 upregulates αA-Crystallin, which is repressed in adult nonlenticular tissues. Conversely, impairment of CY's chaperone activity opposite to the PPIase pocket downregulates a subset of αA-Crystallin's substrates, γ-crystallins. These CY-dependent effects cause age-dependent and chorioretinal-selective declines of ubiquitylated substrates without affecting the chorioretinal morphology. A model emerges whereby inhibition of Ranbp2's CY PPIase remodels crystallins' expressions, subdues molecular aging, and preordains the chorioretina to neuroprotection by augmenting the chaperone capacity and the degradation of polyubiquitylated substrates against proteostatic impairments. Further, the druggable Ranbp2 CY holds pan-therapeutic potential against proteotoxicity and neurodegeneration.

Phosphorylation of RPT6 Controls Its Ability to Bind DNA and Regulate Gene Expression in the Hippocampus of Male Rats during Memory Formation.

Memory formation requires coordinated control of gene expression, protein synthesis, and ubiquitin-proteasome system (UPS)-mediated protein degradation. The catalytic component of the UPS, the 26S proteasome, contains a 20S catalytic core surrounded by two 19S regulatory caps, and phosphorylation of the 19S cap regulatory subunit RPT6 at serine 120 (pRPT6-S120) has been widely implicated in controlling activity-dependent increases in proteasome activity. Recently, RPT6 was also shown to act outside the proteasome where it has a transcription factor-like role in the hippocampus during memory formation. However, little is known about the proteasome-independent function of "free" RPT6 in the brain or during memory formation and whether phosphorylation of S120 is required for this transcriptional control function. Here, we used RNA-sequencing along with novel genetic approaches and biochemical, molecular, and behavioral assays to test the hypothesis that pRPT6-S120 functions independently of the proteasome to bind DNA and regulate gene expression during memory formation. RNA-sequencing following siRNA-mediated knockdown of free RPT6 revealed 46 gene targets in the dorsal hippocampus of male rats following fear conditioning, where RPT6 was involved in transcriptional activation and repression. Through CRISPR-dCas9-mediated artificial placement of RPT6 at a target gene, we found that RPT6 DNA binding alone may be important for altering gene expression following learning. Further, CRISPR-dCas13-mediated conversion of S120 to glycine on RPT6 revealed that phosphorylation at S120 is necessary for RPT6 to bind DNA and properly regulate transcription during memory formation. Together, we reveal a novel function for phosphorylation of RPT6 in controlling gene transcription during memory formation.

Orthogonal approaches required to measure proteasome composition and activity in mammalian brain tissue

Proteasomes are large macromolecular complexes with multiple distinct catalytic activities that are each vital to human brain health and disease. Despite their importance, standardized approaches to investigate proteasomes have not been universally adapted. Here, we describe pitfalls and define straightforward orthogonal biochemical approaches essential to measure and understand changes in proteasome composition and activity in the mammalian central nervous system. Through our experimentation in the mammalian brain, we determined an abundance of catalytically active proteasomes exist with and without a 19S cap(s), the regulatory particle essential for ubiquitin-dependent degradation. Moreover, we learned that in-cell measurements using activity-based probes (ABPs) are more sensitive in determining the available activity of the 20S proteasome without the 19S cap and in measuring individual catalytic subunit activities of each β subunit within all neuronal proteasomes. Subsequently, applying these tools to human brain samples, we were surprised to find that post-mortem tissue retained little to no 19S-capped proteasome, regardless of age, sex, or disease state. In comparing brain tissues (parahippocampal gyrus) from patients with Alzheimer's disease (AD) and unaffected individuals, the available 20S proteasome activity was significantly elevated in severe cases of AD, an observation not previously noted. Taken together, our study establishes standardized approaches for the comprehensive investigation of proteasomes in mammalian brain tissue, and we reveal new insight into brain proteasome biology.

The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates

Proteins are targeted to the proteasome by the attachment of ubiquitin chains, which are markedly varied in structure. Three proteasome subunits–Rpn10, Rpn13, and Rpn1–can recognize ubiquitin chains. Here we report that proteins with single chains of K48-linked ubiquitin are targeted for degradation almost exclusively through binding to Rpn10. Rpn1 can act as a co-receptor with Rpn10 for K63 chains and for certain other chain types. Differences in targeting do not correlate with chain affinity to receptors. Surprisingly, in steady-state assays Rpn13 retarded degradation of various single-chain substrates. Substrates with multiple short ubiquitin chains can be presented for degradation by any of the known receptors, whereas those targeted to the proteasome through a ubiquitin-like domain are degraded most efficiently when bound by Rpn13 or Rpn1. Thus, the proteasome provides an unexpectedly versatile binding platform that can recognize substrates targeted for degradation by ubiquitin chains differing greatly in length and topology.

Proteasomal degradation within endocytic organelles mediates antigen cross-presentation.

During MHC-I-restricted antigen processing, peptides generated by cytosolic proteasomes are translocated by the transporter associated with antigen processing (TAP) into the endoplasmic reticulum, where they bind to newly synthesized MHC-I molecules. Dendritic cells and other cell types can also generate MHC-I complexes with peptides derived from internalized proteins, a process called cross-presentation. Here, we show that active proteasomes within cross-presenting cell phagosomes can generate these peptides. Active proteasomes are detectable within endocytic compartments in mouse bone marrow-derived dendritic cells. In TAP-deficient mouse dendritic cells, cross-presentation is enhanced by the introduction of human β2 -microglobulin, which increases surface expression of MHC-I and suggests a role for recycling MHC-I molecules. In addition, surface MHC-I can be reduced by proteasome inhibition and stabilized by MHC-I-restricted peptides. This is consistent with constitutive proteasome-dependent but TAP-independent peptide loading in the endocytic pathway. Rab-GTPase mutants that restrain phagosome maturation increase proteasome recruitment and enhance TAP-independent cross-presentation. Thus, phagosomal/endosomal binding of peptides locally generated by proteasomes allows cross-presentation to generate MHC-I-peptide complexes identical to those produced by conventional antigen processing.

A neuronal‐specific surface‐exposed membrane proteasome complex modulates neuronal signaling through extracellular signaling peptides

Proteasome‐dependent proteolysis is a tightly regulated process that is essential for life in all archaeal and eukaryotic cells. In the nervous system, proteasome function regulates a wide variety of cellular processes that are critical for proper neuronal function. Largely, the roles of proteasomes in the nervous system have been attributed to modulating the levels of proteins critical for particular cellular processes. However, certain rapidly‐occurring processes such as neuronal transmission, vesicle recycling, and calcium signaling are also affected by acute inhibition of proteasome function. It remains unclear how proteasomes can acutely regulate a cellular process within seconds to minutes, as this remains inconsistent with their canonical role in proteostasis. Here, we made the discovery of a nervous system‐specific membrane proteasome complex that directly and rapidly modulates neuronal function by degrading intracellular proteins into extracellular peptides that can stimulate neuronal signaling. This proteasome complex is tightly associated with the neuronal plasma membrane, exposed to the extracellular space, and is catalytically active. We have determined this complex largely to be made up of 20S proteasome subunits, with little to no 19S cap. Analysis of this membrane proteasome complex by mass spectrometry revealed nervous‐system specific auxiliary membrane glycoproteins which were sufficient for membrane proteasome expression. Selective inhibition of this membrane proteasome complex by a cell‐impermeable proteasome inhibitor blocked extracellular peptide production and attenuated neuronal activity‐induced calcium signaling within seconds. Moreover, membrane proteasome‐derived peptides are sufficient to robustly and rapidly induce neuronal calcium signaling, in part by acting through NMDA receptors. The nature of proteasomal membrane attachment, association with auxiliary transmembrane proteins, exposure to the extracellular space, and capability to signal across the membrane are characteristic of a transmembrane complex. Our discoveries challenge the prevailing notion that proteasomes primarily function to maintain protein homeostasis, and highlight the existence of a form of rapid neuronal communication through a novel transmembrane proteasome complex.Support or Funding InformationThis work was funded by institutional funding and the following grants to S.S.M. (R01 MH102364‐02). K.V.R. was supported by a training grant T32 GM007445 and NSF Graduate Research Fellowship DGE‐1232825.

Regulation of Proteasomal Catalytic Activity by Altering its Protein-Protein Interactions

The proteasome is a central protease of the main intracellular pathway responsible for regulated proteolysis that uses polyubiquitinylation for substrate tagging. The basic functional unit of proteasome called 20S or catalytic particle (CP) is a tube built from four stacked heptameric rings with 3 pairs of catalytic subunits equipped with specific proteolytic activities. The catalytic sites face inside of the tube and are additionally secured by the gates on the tubes’ alpha faces and blocking the access to the CP interior. To get to the active centers, substrates have to bypass the gate, which closed state is affected by binding ligands to the alpha face or catalytic sites. To gain capability to digest polyubiquitinylated substrates, the CP binds a regulatory particle (RP) or a 19S cap to least one site of the tube. The interface between CP and RP allosterically controls dynamics of substrates uptake, digest readiness, and efficiency and specificity of the active centers. The CP also wears other types of caps that allow it to digest efficiently particular populations of substrates and generate certain types of products. Also in these cases the interface between the protein complexes plays a crucial regulatory role. Here we designed a range of peptides, peptidomimetics and small molecule compounds that affect these protein – protein interactions to study selected mechanical aspects of proteasomal regulation. Using spectroscopic and microscopic tools we found that binding of certain ligands may affect status of the proteasomal gate, alpha face conformation, stability of the complexes or/and the CP dynamics. These structural changes alter the enzyme activity and specificity, which in turn influence intracellular metabolism. We attempted to correlate particular biological effects of the ligands with their mode of molecular action and their chemical properties.

The Cdc48–Vms1 complex maintains 26S proteasome architecture

The 26S proteasome is responsible for most regulated protein turnover and for the degradation of aberrant proteins in eukaryotes. The assembly of this ~2.5 MDa multicatalytic protease requires several dedicated chaperones and, once assembled, substrate selectivity is mediated by ubiquitin conjugation. After modification with ubiquitin, substrates are escorted to the proteasome by myriad factors, including Cdc48 (cell-division cycle 48). Cdc48 also associates with numerous cofactors, but, to date, it is unclear whether each cofactor facilitates proteasome delivery. We discovered that yeast lacking a conserved Cdc48 cofactor, Vms1 [VCP (valosin-containing protein)/Cdc48-associated mitochondrial stress-responsive], accumulate proteasome-targeted ubiquitinated proteins. Vms1 mutant cells also contain elevated levels of unassembled 20S proteasome core particles and select 19S cap subunits. In addition, we found that the ability of Vms1 to support 26S proteasome assembly requires Cdc48 interaction, and that the loss of Vms1 reduced 26S proteasome levels and cell viability after prolonged culture in the stationary phase. The results of the present study highlight an unexpected link between the Cdc48-Vms1 complex and the preservation of proteasome architecture, and indicate how perturbed proteasome assembly affects the turnover of ubiquitinated proteins and maintains viability in aging cells.

Inherent Asymmetry in the 26S Proteasome Is Defined by the Ubiquitin Receptor RPN13

The 26S double-capped proteasome is assembled in a hierarchic event that is orchestrated by dedicated set of chaperons. To date, all stoichiometric subunits are considered to be present in equal ratios, thus providing symmetry to the double-capped complex. Here, we show that although the vast majority (if not all) of the double-capped 26S proteasomes, both 19S complexes, contain the ubiquitin receptor Rpn10/S5a, only one of these 19S particles contains the additional ubiquitin receptor Rpn13, thereby defining asymmetry in the 26S proteasome. These results were validated in yeast and mammals, utilizing biochemical and unbiased AQUA-MS methodologies. Thus, the double-capped 26S proteasomes are asymmetric in their polyubiquitin binding capacity. Our data point to a potential new role for ubiquitin receptors as directionality factors that may participate in the prevention of simultaneous substrates translocation into the 20S from both 19S caps.

Abstract P4-05-11: A proteasomal signature of breast cancer cells

Abstract The multisubunit, multifunctional protease called proteasome as a part of the essential proteasome-ubiquitin pathway constitutes an attractive target for anti-cancer drugs. A proteasome inhibitor bortezomib is successful in blood cancers treatment, however trials with breast cancers yield disappointingly inconsistent results, likely stemming from the cancers’ diversity. Since bortezomib preferentially induces an apoptosis in cancerous cells, it is likely that differences in the proteasome pathway between the control and cancerous cells, and also between distinct cancers, contribute to this effect. Here we compared components of proteasome assemblies and their peptidase activities in seven breast cancer and two control cell lines in an attempt to find a common proteasomal signature of breast cancer. Defining a common proteolytic denominator for breast cancer cells should facilitate a rational drug design based on proteasomal inhibition. For this purpose, we analyzed cytosolic, nuclear and microsomal extracts from human cultured breast cells: control (MCF10A, Hs 578 Bst) and derived from distinct types of breast cancer: luminal A MCF7 and T47D, triple negative basal A MDA-MB-468, and triple negative basal B MDA-MB-231, Hs 578 T and BT-549. We found a high content of total proteasome in a microsomal fraction with a relatively prominent contribution from immuno proteasomes in all cancer cell lines. These proteasomes are believed to be localized on the outside of endoplasmic reticulum membrane and presumably take part in the endoplasmic reticulum - associated degradation system. Markedly, the pattern of peptidase activities of proteasome and content of subunits of its exchangeable sub-assemblies were specific for each fraction and discriminated between cancerous and control cells. Statistical analysis identified two clusters formed by the cell lines in the microsomal and nuclear fractions and a distinct clustering of the cytosols. Furthermore, three groups of variables, which tend to always cluster together were identified: the 19S regulatory particle subunits, immunoproteasome subunits and peptidolytic activities. Variables that the best quantitatively discriminate between the cell lines at a given level of total proteasome were immunoproteasome subunits and 19S cap subunit Rpt5. Additionally, the housekeeping subunit beta5 in the cytosol, the PA28 activator gamma subunit in the microsomal fraction and chymotrypsin like activity in the nuclear fraction qualitatively were the best markers aiding classification of the cell lines. We speculate that the distinct properties of proteasomes in the microsomal and nuclear fractions may contribute to specific response of the cancer cell lines to the treatment with proteasomal inhibitors. The study shows that a comprehensive analysis of the proteasome system in the established breast cancer cell lines may help to guide diagnostics and therapy design. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-11.

Inhibition Of The Deubiquitinating Enzymes UCHL5 and USP14 Is Lethal To Waldenströms Macroglobulinemia Cells

BackgroundWaldenströms macroglobulinemia (WM) is a lymphoplasmacytic subtype of Non-Hodgkins lymphoma in which specific molecular changes lead to unrestricted cell proliferation and overproduction of immunoglobulin-M. These processes require exquisite coordination between growth promoting transcription factors (NFkB) and cell homeostatic systems. The bioavailability of various transcription factors and cell cycle proteins is primarily regulated by the ubiquitin proteasome system (UPS). Moreover, the proteolytic machinery ensures proper elimination of unwanted or misfolded proteins, which when disrupted leads to protein accumulation and apoptotic cell death. The 26S proteasome is a barrel shaped structure with a 20S catalytic core that is flanked by 19S caps on either side. 26S proteasomes are critical for WM cell survival, which is clinically evident, as up to 80% of WM patients treated with the proteasome inhibitor (PI) bortezomib have derived significant benefit. Traditional PI such as bortezomib and carfilzomib have been designed to target the B5 catalytic core within the 26S proteasome. However, proteasomes are capable of altering conformation of their proteolytic subunits in response to inflammation and stress, which can lower the effectiveness of these PI. The 19S cap is the regulatory complex and functions in unfolding and deubiquitinating the proteins before their entry into the 20S complex using constitutive deubiquitinating enzymes (DUBS). Recently, it has been demonstrated that inhibition of the DUBS, UCHL5 and USP14 results in cell death in a variety of tumor types but more so in cancer cells that rapidly divide or have a high protein turnover rate. AimTo define the anti-WM activity of the novel DUB inhibitor, b-AP15 in preclinical models of WM. MethodsThe WM cell lines BCWM.1, RPCI-WM1 and MWCL-1 were used for experiments in this analysis. Proteasomal activity was measured using synthetic fluorogenic peptide substrates. Apoptosis was determined by annexin-V/PI staining and mitochondrial membrane permeability (MOMP) was assessed using TMRM followed by flow cytometry. Protein profiling was done via immunoblot analysis. ResultsAs reported by D'Arcy et al in their characterization of the b-AP15 molecule, inhibition of UCHL5 and USP14 by b-AP15 does not disrupt proteasomal activity conferred by the b-catalytic subunits. We confirmed these findings by treating WM cells with single agent bortezomib (10nM), carfilzomib (10nM), b-AP15 (100nM) or all three agents in combination to assess chymotrypsin-like, caspase-like and trypsin-like proteasomal activity using fluorogenic peptide substrates. Further, when used in combination with the other PI, PI-mediated chymotrypsin-like activity remained inhibited in the presence of b-AP15. Next, we sought to determine if b-AP15 treatment could induce WM cell death. Annexin-v staining showed that b-AP15 (500uM) induced apoptosis in all WM cell lines (28 – 60% cell death) with variable responses noted among the 3 models. Treatment with b-AP15 increased MOMP while also inducing the cleavage of caspases-9 and 3 and PARP-1 suggesting that the anti-WM activity of b-AP15 is mediated through the intrinsic apoptotic pathway. As components of the NFkB signaling cascade lie downstream to the UPS, we examined the effects of b-AP15 on this pathway. When treated with the DUB-inhibitor, nuclear translocation of NFkB was reduced in a time dependent manner. Interestingly, treatment with b-AP15 increased the phosphorylation of the mitogen activated protein kinase-p38 (p38) in all the WM cell lines tested. Treatment of WM cells with b-AP15 in presence of the p38 inhibitor, SB203580, resulted in a synergistic induction of cell death.Conclusionb-AP15 is a novel DUB inhibitor that disrupts two regulatory enzymes (UCHL5 and USP14) present in the 19S proteasomal cap. Results presented here demonstrate that b-AP15 induces apoptosis in in vitro models of WM and with in vivo analysis underway, is a potential therapeutic in WM.We would like to acknowledge the Waterfall Waldenström Macroglobulinemia Research Fund, the Leukemia and Lymphoma Society and the International Waldenström Macroglobulinemia Foundation for their continued support. Disclosures:No relevant conflicts of interest to declare.

The Deubiquitinating Enzymes Of The 19S Proteasome Offer Novel Therapeutic Opportunity In Bortezomib Resistant Waldenströms Macroglobulinemia

Background The ubiquitin proteasome system (UPS) maintains homeostasis in eukaryotic cells by degrading and recycling proteins associated with DNA transcription and cell cycle regulation. In tumor cells with a high protein turnover rate, particularly in immunoglobulin secreting cancers such as Waldenströms Macroglobulinemia (WM), proteasomes are critical for sustained cell proliferation. Proteasome inhibitors (PI) such as bortezomib and carfilzomib target the B5 subunit of the proteasome catalytic core and disrupt its activity leading to accumulation of polyubiquitinated proteins. Although highly effective in WM, persistent use of bortezomib eventually leads to emergence of a bortezomib resistant (BR) subclone. Point mutation in the PSMB5 gene (encoding the B5 subunit) leading to altered binding kinetics is identified as a potential underlying mechanism of PI resistance. Despite these adaptive modifications that support resistance to PI resistance, the UPS as a whole remains a relevant target with vulnerable sites that can be therapeutically exploited. The 19S cap of the proteasome contains deubiquitinating enzymes (DUBS) that function to deubiquitinate proteins prior to their entry into the proteasomal core. Using a novel DUB-inhibitor b-AP15, which blocks the UCHL5 and USP14 DUBS, D’Arcy et al demonstrated that disruption of these DUBS does not alter proteasomal activity yet induces robust tumor cell death in various cancers. Aim Investigation of b-AP15 in preclinical models of BR WM and characterization of associated downstream signaling interactions. Methods For these studies, we developed and used BR variants of the most commonly used WM cell lines (variants termed BCWM.1/BR, RPCI-WM1/BR and MWCL-1/BR). Proteasomal activity was measured in these cells using synthetic fluorogenic peptide substrates and apoptosis was measured by annexin-v/PI staining. For gene expression profiling (GEP), the Nanostring nCounter mRNA quantification assay was utilized. Results We treated all BR WM clones with either single agent bortezomib (10nM), carfilzomib (10nM), b-AP15 (100nM) or all three agents in combination and assessed their effect on chymotrypsin-like, caspase-like and trypsin-like proteasomal activity. b-AP15, either alone or in combination with the other PI, did not alter proteasomal activity, nor did it abrogate the inhibition of chymotrypsin-like activity of other PI. Although proteasomal activity was not disrupted, we observed an increase in high molecular weight ubiquitinated proteins on immunoblot analysis. We hypothesized that despite the BR cells resistance to B5-targeting PI, they would remain sensitive to UPS inhibition if targeted through DUB inhibition. We treated BR cells with b-AP15 at concentrations ranging from 50nM - 1.25uM and observed that b-AP15 induced robust WM cell death in a dose and time dependent manner. Apoptosis was more pronounced in MWCL-1/BR cells and optimal cell death (55%) was observed at 500nM; however a commitment towards cellular demise was evident by PARP-1 and caspase cleavage as early as 3 hrs. Use of a pan-caspase inhibitor resulted in rescuing of the BR WM cells from b-AP15 mediated death and demonstrated a caspase-dependent death process. In order to gain further mechanistic insight into the processes that regulates response to b-AP15, we performed GEP and immunoblot of BR WM cells treated with 50nM of b-AP15. We observed an increase in phospho-p38 protein, which belongs to the MAPK family and regulates IL8 secretion. When BR WM cells were treated with a p38 inhibitor in combination with b-AP15, a significant decrease in cell viability was noted relative to b-AP15 (100nM) alone. Furthermore, GEP and network analysis identified key regulator genes associated with p53, cell cycle and MAPK signaling. Summary We provide first evidence that inhibition of the DUBS, UCHL5 and USP14 with b-AP15 results in caspase-dependent apoptosis of BR WM cells. Our investigation uncovers important molecular interactions that may dictate the BR cells responsiveness to DUB-inhibition by b-AP15. These observations validate the pervasive role of the UPS and confirm alternate therapeutics targets using our unique BR WM models. We are grateful to the Waterfall Waldenström Macroglobulinemia Research Fund, the Leukemia and Lymphoma Society and the International Waldenström Macroglobulinemia Foundation for their continued support. Disclosures: Martin: Teva: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Genentech: Speakers Bureau; Millennium: Research Funding; Seattle Genetics: Consultancy, Speakers Bureau.

Rapamycin Allosterically Inhibits the Proteasome

Rapamycin is a canonical allosteric inhibitor of the mammalian tarpet of rapamycin (mTOR) kinase with immunosuppressive and proapoptotic activities. We found that in vitro rapamycin also regulates the proteasome, which is an essential intracellular protease of the ubiquitin-proteasome pathway. Rapamycin inhibits proteinase and selected peptidase activities of the catalytic core proteasome at low micromolar concentrations. Moreover, the drug interferes with binding of the 19S cap essential for processing of polyubiquitinylated substrates and with the PA200 proteasome activator to the 20S catalytic core proteasome. These protein complexes are known to bind to specific grooves on the α face region of the 20S core. Treatment with rapamycin affects the conformational dynamics of the proteasomal gate, which is centrally positioned within the α face and allosterically regulated element responsible for the intake of substrates. We showed that rapamycin shares all the proteasome targeting properties not only with other two-domain, closed-ring analogs (rapalogs) but also with its single domain mimics and seco-rapamycin, which is the first in vivo open-ring metabolite of rapamycin that does not affect mTOR. We hypothesize that rapamycin and related compounds bind to the α face and allosterically impact proteasome function. This article discusses the implications of our findings for the mechanism of in vivo actions of rapamycin and for the design of novel allosteric drugs targeting the proteasome.

Knockdown of human deubiquitinase PSMD14 induces cell cycle arrest and senescence

The PSMD14 (POH1, also known as Rpn11/MPR1/S13/CepP1) protein within the 19S complex (19S cap; PA700) is responsible for substrate deubiquitination during proteasomal degradation. The role of PSMD14 in cell proliferation and senescence was explored using siRNA knockdown in carcinoma cell lines. Our results reveal that down-regulation of PSMD14 by siRNA transfection had a considerable impact on cell viability causing cell arrest in the G0-G1 phase, ultimately leading to senescence. The molecular events associated with decreased cell proliferation, cell cycle arrest and senescence include down-regulation of cyclin B1–CDK1–CDC25C, down-regulation of cyclin D1 and up-regulation of p21 /Cip and p27 /Kip1. Most notably, phosphorylation of the retinoblastoma protein was markedly reduced in PSMD14 knockdown cells. A comparative study with PSMB5, a subunit of the 20S proteasome, revealed that PSMB5 and PSMD14 have different effects on cell cycle, senescence and associated molecular events. These data support the view that the 19S and 20S subunits of the proteasome have distinct biological functions and imply that targeting 19S and 20S would have distinct molecular consequences on tumor cells.

Proteasome subunits are regulated and expressed in comparable concentrations as a functional cluster

The proteasome is the main proteolytic enzyme that functions in the ubiquitin–proteasome system. The 26S proteasome has multi-subunit protease complexes consisting of 20S subunits composed of four seven-numbered rings with two outer rings containing α subunits and two central rings composed of β subunits, and 19S caps of 6 ATPase and 11 non-ATPase subunits; however, it is unclear how these subunits are regulated and the 26S proteasomes assembled. To verify whether each subunit’s mRNA expression is associated with the mRNA expression of other proteasome subunits, we carried out expression analysis of 34 proteasome subunits mRNA on peripheral blood from 75 subjects. The expression of proteasome subunits mRNA was comparable in each individual of the studied population and the mRNA expression has been investigated in each 20S or 19S proteasome. Our results suggest that each type of subunit is regulated by respectively common factors, and that the 20S and 19S proteasomes are regulated by different systems.

Role for proteasome activator PA200 and postglutamyl proteasome activity in genomic stability

Proteasome activator PA200 enhances proteasome-mediated cleavage after acidic residues in vitro; however, its role within cells is not known. Here, we show that, in response to ionizing radiation, PA200 forms hybrid proteasomes with 19S caps and 20S core proteasomes that accumulate on chromatin, leading to an increase in proteolytic activity. Unlike many other proteins that respond to DNA damage, the response of PA200 appears to be independent of Ataxia Telangiectasia Mutated and p53, but dependent on DNA-dependent protein kinase activity. Nonetheless, PA200 is critical because PA200-knockdown cells show genomic instability and reduced survival after exposure to ionizing radiation. This phenotype is reproduced by specific inhibition of postglutamyl activity of proteasomes, but combined treatment with PA200 siRNA and postglutamyl inhibitor does not show additive effects on survival. Together, these data suggest a unique role for PA200 in genomic stability that is likely mediated through its ability to enhance postglutamyl cleavage by proteasomes.

Hsp90-mediated Assembly of the 26 S Proteasome Is Involved in Major Histocompatibility Complex Class I Antigen Processing

Heat shock protein 90 (hsp90) and the proteasome activator PA28 stimulate major histocompatibility complex (MHC) class I antigen processing. It is unknown whether hsp90 influences the proteasome activity to produce T cell epitopes, although association of PA28 with the 20 S proteasome stimulates the enzyme activity. Here, we show that hsp90 is essential in assembly of the 26 S proteasome and as a result, is involved in epitope production. Addition of recombinant hsp90alpha to cell lysate enhanced chymotrypsin-like activity of the 26 S proteasome in an ATP-dependent manner as determined by an in-gel hydrolysis assay. We successfully pulled down histidine-tagged hsp90alpha- and PA28alpha-induced, newly assembled 26 S proteasomes from the cell extracts for in vitro epitope production assay, and we found these structures to be sensitive to geldanamycin, an hsp90 inhibitor. We found a cleaved epitope unique to the proteasome pulled down by both hsp90alpha and PA28alpha, whereas two different epitopes were identified in the hsp90alpha- and PA28alpha-pulldowns, respectively. Processing of these respective peptides in vivo was enhanced faithfully by the protein combinations used for the proteasome pulldowns. Inhibition of hsp90 in vivo by geldanamycin partly disrupted the 26 S proteasome structure, consistent with down-regulated MHC class I expression. Our results indicate that hsp90 facilitates MHC class I antigen processing through epitope production in a complex of the 26 S proteasome.

Protein quality control and ubiquitin proteasome system: implications on cataract

Abstract Purpose Accumulation of damaged or abnormal proteins is cytotoxic and is causally related to various age‐related diseases, including cataract. The objective of this study is to investigate the effect of 19S regulatory complexes on the fate of damaged proteins. Methods The denaturation of firefly luciferase (a model protein) was performed at 43°C during 10 min in the presence of Hsp90 and denaturation of luciferase was monitored by the loss of its enzymatic activity. Luciferase activity in the cells was determined to monitor the refolding of denatured luciferase at 30°C in the presence or absence of ubiquitination system. Results The data showed that heat‐denatured luciferase was preferentially ubiquitinated and degraded by the UPP as compared with the native form. Inhibition of the ubiquitination or proteolysis enhanced renaturation. The 19S regulatory complex enhances renaturation of denatured substrate in the presence of ubiquitinating activity. The data also suggested that recognition of a poliubiquitinated substrate requires that polyubiquitin chain interact with specific domains of the 19S cap of the proteasome and this interaction play an important role on the fate of denatured proteins. Additionally, the data shown that are critical lysines in the ubiquitin moiety are required for an efficient and productive interaction with proteasome. Conclusion Failure in the protein quality control system is likely to have important implication in loss of lens transparency and cataract formation.

The Cyclophilin-like Domain of Ran-binding Protein-2 Modulates Selectively the Activity of the Ubiquitin-Proteasome System and Protein Biogenesis

The ubiquitin-proteasome system (UPS) plays a critical role in protein degradation. The 19S regulatory particle (RP) of the 26S proteasome mediates the recognition, deubiquitylation, unfolding, and channeling of ubiquitylated substrates to the 20S proteasome. Several subunits of the 19S RP interact with a growing number of factors. The cyclophilin-like domain (CLD) of Ran-binding protein-2 (RanBP2/Nup358) associates specifically with at least one subunit, S1, of the base subcomplex of the 19S RP, but the functional implications of this interaction on the UPS activity are elusive. This study shows the CLD of RanBP2 promotes selectively the accumulation of a subset of reporter substrates of the UPS, such as the ubiquitin (Ub)-fusion yellow fluorescent protein (YFP) degradation substrate, Ub(G76V)-YFP, and the N-end rule substrate, Ub-R-YFP. Conversely, the degradation of endoplasmic reticulum and misfolded proteins, and of those linked to UPS-independent degradation, is not affected by CLD. The selective effect of CLD on the UPS in vivo is independent of, and synergistic with, proteasome inhibitors, and CLD does not affect the intrinsic proteolytic activity of the 20S proteasome. The inhibitory activity of CLD on the UPS resides in a purported SUMO binding motif. We also found two RanBP2 substrates, RanGTPase-activating protein and retinitis pigmentosa GTPase regulator interacting protein-1alpha1, whose steady-state levels are selectively modulated by CLD. Hence, the CLD of RanBP2 acts as a novel auxiliary modulator of the UPS activity; it may contribute to the molecular and subcellular compartmentation of the turnover of properly folded proteins and modulation of the expressivity of several neurological diseases.

Cdc48 (p97): a ‘molecular gearbox’ in the ubiquitin pathway?

Cdc48 (p97), a conserved chaperone-like ATPase of eukaryotic cells, has attracted attention recently because of its wide range of cellular functions. Cdc48 is intimately linked to the ubiquitin pathway because its primary action is to segregate ubiquitinated substrates from unmodified partners. This 'segregase' activity is crucial for certain proteasomal degradation pathways and for some nonproteolytic functions of ubiquitin. Cdc48 associates not only with different 'substrate-recruiting cofactors' but also with distinct 'substrate-processing cofactors'. The latter proteins control the degree of ubiquitination of bound substrates by shifting the polyubiquitination reaction into 'forward', 'neutral' or 'reverse'. We discuss how Cdc48 might use this 'gearbox activity' to control protein fate and propose a similar mode of action for the 19S cap of the proteasome.