Reaction of 20S proteasome: shift of SDS-dependent activation profile by divalent cations

Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties

Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases.

Human Sex Determination at the Edge of Ambiguity: INHERITED XY SEX REVERSAL DUE TO ENHANCED UBIQUITINATION AND PROTEASOMAL DEGRADATION OF A MASTER TRANSCRIPTION FACTOR

A general problem is posed by analysis of transcriptional thresholds governing cell fate decisions in metazoan development. A model is provided by testis determination in therian mammals. Its key step, Sertoli cell differentiation in the embryonic gonadal ridge, is initiated by SRY, a Y-encoded architectural transcription factor. Mutations in human SRY cause gonadal dysgenesis leading to XY female development (Swyer syndrome). Here, we have characterized an inherited mutation compatible with either male or female somatic phenotypes as observed in an XY father and XY daughter, respectively. The mutation (a crevice-forming substitution at a conserved back surface of the SRY high mobility group box) markedly destabilizes the domain but preserves specific DNA affinity and induced DNA bend angle. On transient transfection of diverse human and rodent cell lines, the variant SRY exhibited accelerated proteasomal degradation (relative to wild type) associated with increased ubiquitination; in vitro susceptibility to ubiquitin-independent ("default") cleavage by the 20S core proteasome was unchanged. The variant's gene regulatory activity (as assessed in a cellular model of the rat embryonic XY gonadal ridge) was reduced by 2-fold relative to wild-type SRY at similar levels of mRNA expression. Chemical proteasome inhibition restored native-like SRY expression and transcriptional activity in association with restored occupancy of a sex-specific enhancer element in principal downstream gene Sox9, demonstrating that the variant SRY exhibits essentially native activity on a per molecule basis. Our findings define a novel mechanism of impaired organogenesis, accelerated ubiquitin-directed proteasomal degradation of a master transcription factor leading to a developmental decision poised at the edge of ambiguity.

The proteasome and its role in the degradation of oxidized proteins

The generation of free radicals and the resulting oxidative modification of cell structures are omnipresent in mammalian cells. This includes the permanent oxidation of proteins leading to the disruption of the protein structure and an impaired functionality. In consequence, these oxidized proteins have to be removed in order to prevent serious metabolic disturbances. The most important cellular proteolytic system responsible for the removal of oxidized proteins is the proteasomal system. For normal functioning, the proteasomal system needs the coordinated interaction of numerous components. This review describes the fundamental functions of the 20S "core" proteasome, its regulators, and the roles of the proteasomal system beyond the removal of oxidized proteins in mammalian cells.

Inhibition of the 20S proteosome by a protein proteinase inhibitor: evidence that a natural serine proteinase inhibitor can inhibit a threonine proteinase

The 20S proteasome (20S) is an intracellular threonine proteinase (Mr 750,000) that plays important roles in many cellular regulations. Several synthetic peptide inhibitors and bacteria-derived inhibitors such as lactacystin and epoxomicin have been identified as potent proteasome inhibitors. However, essentially no protein proteinase inhibitor has been characterized. By examining several small size protein proteinase inhibitors, we found that a well-known serine proteinase inhibitor from bovine pancreas, basic pancreatic trypsin inhibitor (BPTI), inhibits the 20S in vitro and ex vivo. Inhibition of the 20S by BPTI was time- and concentration-dependent, and stoichiometric. To inhibit the 20S activity, BPTI needs to enter into the interior of the 20S molecule. The molar ratio of BPTI to the 20S in the complex was estimated as approximately six BPTI to one 20S, thereby two sets of three peptidase activities (trypsin-like, chymotrypsin-like and caspase-like) of the 20S were all inhibited. These results indicate that an entrance hole to the 20S formed by seven alpha-subunits is sufficiently large for BPTI to enter. This report is essentially the initial description of the inhibition of a threonine proteinase by a protein serine proteinase inhibitor, suggesting a common mechanism of inhibition between serine and threonine proteinases by a natural protein proteinase inhibitor.

Functional and biochemical characterization of the 20S proteasome in a yeast temperature-sensitive mutant, rpt6-1

Background

Rpt6-1 is a thermosensitive yeast mutant with a deletion of a gene encoding a regulatory subunit of the 26S proteasome, RPT6, which is able to grow at 25°C but not at 37°C. In this study, peptidase activities, activation profiles, and the subunit composition of the 20S proteasome purified from the rpt6-1 mutant was characterized.

Results

The 20S proteasome purified from rpt6-1 exhibited low levels of peptidase activities in the absence of activators, but nearly same activated activities in the presence of activators, suggesting a gating defect in the proteasome channel. Detailed analyses of the composition of the 20S proteasome through separation of all subunits by two-dimensional gel electrophoresis followed by identification of each subunit using MALDI-TOF-MS revealed that two subunits, α1 and α7, differed from those of wild-type cells in both electrophoretic mobility and pI values. The changes in these two α-subunits were apparent at the permissive temperature, but disappeared during stress response at the restrictive temperature. Interestingly, upon disappearance of these changes, the levels of peptidase activity of the 20S proteasome in the rpt6-1 mutant were restored as the wild-type. These results suggest that two different forms of the α-subunits, α1 and α7, block the proteasome channel in the rpt6-1 mutant.

Conclusion

Two α-subunits (α1 and α7) of the 20S proteasome in the rpt6-1 mutant differed from their wild-type counterparts and peptidase activities were found to be lower in the mutant than in the wild-type strain.

Development of an enzyme-linked immunosorbent assay for the pyrethroid insecticide cyhalothrin

A competitive enzyme-linked immunosorbent assay (ELISA) was developed for detection of the pyrethroid insecticide cyhalothrin. Three haptens with an amine or propanoic acid terminus were synthesized and then conjugated with bovine serum albumin to give immunogens. Eight polyclonal antisera produced by rabbits were screened for titers and affinity using three different coating antigens. The antiserum CWB-C had the highest affinity with cyhalothrin and a low affinity with fenvalerate, fenpropathrin, deltamethrin, and fluvalinate. The half-maximum inhibition concentration for cyhalothrin was 37.2 microg/L, and the limit of detection was 4.7 microg/L. The recoveries of different concentrations of cyhalothrin (0.1-2500 microg/L) from fortified tap water, well water, and wastewater samples as determined with the ELISA were 81-114%.

Effect of temperature and pressure on the proteolytic specificity of the recombinant 20S proteasome from Methanococcus jannaschii

The hydrolytic specificity of the recombinant 20S proteasome from the deep-sea thermophile Methanococcus jannaschii was evaluated toward oxidized insulin B-chain across a range of temperatures (35 degrees, 55 degrees, 75 degrees, and 90 degrees C) and hydrostatic pressures (1, 250, 500, and 1,000 atm). Of the four temperatures considered, the same maximum overall hydrolysis rate was observed at both 55 degrees and 75 degrees C, which are much lower than the T(opt) of 116 degrees C previously observed for a small amide substrate (Michels and Clark 1997). At 35 degrees C the rates of cleavage were highest at the carboxyl side of glutamine and leucine, whereas at the three higher temperatures, the most rapid cleavages occurred after leucine and glutamic acid residues. The distribution of proteolytic fragments and the cleavage sequence also varied between the lowest and higher temperatures. Application of hydrostatic pressure did not increase proteasome activity, as observed previously for the amide substrate (Michels and Clark 1997), but instead significantly reduced the overall conversion of the polypeptide substrate. Overall cleavage patterns observed for the recombinant M. jannaschii proteasome were similar to those reported previously for Thermoplasma acidophilum (Akopian et al. 1997) and human proteasomes (Dick et al. 1991), indicating that proteasome specificity has been conserved despite significant environmental diversity.

Atomic force microscopy studies of interaction of the 20S proteasome with supported lipid bilayers

The 20S proteasome plays important roles in degradation of intracellular proteins. Mechanisms of its activation, its localization in cells, and its binding to biomembranes are not well understood. In this study, we used atomic force microscopy (AFM) to investigate interactions between the 20S proteasome and supported bilayers of various lipids in a buffer. We found that the 20S proteasome specifically bound to supported bilayers containing phosphatidylinositol (PI), but did not bind to supported bilayers containing phosphatidylcholine, phosphatidic acid or dioleoyltrimethylammonium propane. Binding of the 20S proteasomes had a high orientation; almost all were in a top view position. The specific and orientational binding of the 20S proteasome with PI may play important roles inside cells such as endoplasmic reticulum (ER) membrane. Use of AFM to study supported bilayers provides new information on ligand-receptor interactions.

The bovine lung 20S proteasome binding to reversible inhibitors: modulation by sodium ion

The effect of sodium ion on the inhibition exerted by Cbz-Leu-Leu-Leu-CHO on the chymotrypsin-like activity of the 20S proteasome isolated from bovine lung was investigated. The experimental data were analyzed using a standard linkage formalism. The calculated equilibrium affinity constants for the sodium ion binding to the free-enzyme and the inhibitor-bound enzyme are compatible to other well-characterized ion-involving heterotropic systems. The functional interdependence between the binding events played by the inhibitor and the sodium ion conforms to a heterotropic modulatory mechanism.

Structure--function relationships in bovine thymus 20S proteasome: a fluorimetric study

The structure--function relationships occurring on the bovine thymus 20S proteasome, which exhibits the features of an immunoproteasome, have been studied. The investigation has been performed, essentially, using a fluorimetric approach, taking advantage either of the sensitivity of the complex to sodium dodecil sulfate and chaotropic agents (urea and guanidine hydrochloride) or of the presence, on the molecule, of a high number of tryptophan residues. The results obtained indicate that the perturbation or the oxidation of these residues affect the catalytic events taking place on the thymus proteasome and that the functional effects determined by SDS and chaotropic agents most likely occur through a series of progressive structural modifications leading to an inactive molecule. The presence of structural intermediates in the proteasome inactivation process suggests that thymus proteasome is a molecule characterized, at the same time, by structural flexibility (modulation of active sites) and structural stability (maintaining of the quaternary structure) in agreement with its crucial role in the cell life cycle.

Activation of the 20S proteasome of Xenopus oocytes by cardiolipin: blockage of the activation of trypsin-like activity by the substrate

The effects of an activator, cardiolipin, on the three peptidase activities of the 20S proteasome of Xenopus oocytes were examined. The trypsin-like activity was activated when the enzyme was treated with cardiolipin before the addition of the substrate, but there was no appreciable activation when cardiolipin was added concomitantly with the substrate. On the other hand, the chymotrypsin-like peptidase and peptidylglutamylpeptide hydrolase (PGPH) were activated regardless of the sequence of addition. When very low concentrations of the substrate (e.g. 0.1-0.5 microM; about 1/100 of the K(m)) were used, cardiolipin strongly activated trypsin-like peptidase by the simultaneous addition but not after substrate addition. These results suggest that the trypsin-type substrate produces a conformational change in the enzyme in a concentration-dependent manner which makes the activator sites inaccessible to cardiolipin.

Purification and characterization of an SDS-activated fibrinolytic enzyme from Eisenia fetida

A sodium-dodecyl-sulfate-activated fibrinolytic enzyme from Eisenia fetida (the E. fetida enzyme) was purified by chromatography on DEAE Sepharose, Sephadex G-75, and Phenyl Sepharose 4. It (M(r) = 45 kDa) was composed of two subunits (M(r) = 26 kDa and M(r) = 18 kDa) held together by hydrophobic interactions. The enzyme displayed four activities when we used fibrin plates to detect the proteolytic activity. These were designated as CFPg (complete fibrinolysis in the plasminogen-rich plate), uCFPg (uncompleted fibrinolysis in the plasminogen-rich plate), CF (complete fibrinolysis in the plasminogen-free plate), and uCF (uncompleted fibrinolysis in the plasminogen-free plate). SDS activated CFPg and rendered the enzyme more sensitive to some inhibitors. Leupeptin, chymostatin, pepstatin, aprotinin, phenylmethylsulfonyl fluoride, and dithiothreitol had no effect on uCF. Pepstatin stimulated CFPg and uCFPg, while E-64, a thiol inhibitor, activated uCFPg and uCF. The N-terminal sequence of the large subunit was analyzed and compared with some known proteins. The large subunit alone had catalytic activity, while the small subunit did not. Using plasminogen as the substrate for defining peptide bond specificity, the E. fetida enzyme was observed to cleave the carboxyl side of basic amino acids, small neutral amino acids, and Met residue.