Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11

The ATP-dependent degradation of polyubiquitylated proteins by the 26S proteasome is essential for the maintenance of proteome stability and the regulation of a plethora of cellular processes. Degradation of substrates is preceded by the removal of polyubiquitin moieties through the isopeptidase activity of the subunit Rpn11. Here we describe three crystal structures of the heterodimer of the Mpr1–Pad1–N-terminal domains of Rpn8 and Rpn11, crystallized as a fusion protein in complex with a nanobody. This fusion protein exhibits modest deubiquitylation activity toward a model substrate. Full activation requires incorporation of Rpn11 into the 26S proteasome and is dependent on ATP hydrolysis, suggesting that substrate processing and polyubiquitin removal are coupled. Based on our structures, we propose that premature activation is prevented by the combined effects of low intrinsic ubiquitin affinity, an insertion segment acting as a physical barrier across the substrate access channel, and a conformationally unstable catalytic loop in Rpn11. The docking of the structure into the proteasome EM density revealed contacts of Rpn11 with ATPase subunits, which likely stabilize the active conformation and boost the affinity for the proximal ubiquitin moiety. The narrow space around the Rpn11 active site at the entrance to the ATPase ring pore is likely to prevent erroneous deubiquitylation of folded proteins.In eukaryotes, the ubiquitin (Ub) proteasome system (UPS) is responsible for the regulated degradation of proteins (1–5). The UPS plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer needed. Consequently, the UPS is critically involved in numerous cellular processes, including cell cycle progression, apoptosis, and DNA damage repair, and malfunctions of the system often result in disease.The 26S proteasome executes the degradation of substrates that are marked for destruction by the covalent attachment of polyubiquitin chains. It is a molecular machine of 2.5 MDa comprising two subcomplexes, the 20S core particle (CP) and one or two 19S regulatory particles (RPs), which associate with the ends of the cylinder-shaped CP (6–8). The recognition and recruitment of polyubiquitylated substrates, their deubiquitylation, ATP-dependent unfolding, and translocation into the core particle take place in the RP. The structurally and mechanistically well-characterized CP houses the proteolytic activities and sequesters them from the environment, thereby avoiding collateral damage (9).The RPs attach to the outer α-rings of the CP, which control access to the proteolytic chamber formed by the inner β-subunit rings (10). Recently, the molecular architecture of the 26S holocomplex was established using cryo-EM–based approaches (11, 12), and a pseudoatomic model of the holocomplex was put forward (13). The RP is formed by two subcomplexes, known as the base and the lid, which assemble independently (12, 14). The base contains the hetero-hexameric AAA-ATPase ring (Rpt1–Rpt6), which drives the conformational changes required for substrate processing, including unfolding and translocation into the CP (15, 16). The base also contains the largest RP non-ATPase subunits, Rpn1 and Rpn2, and the Ub receptor Rpn13. The second resident Ub receptor, Rpn10, is not part of either the base or the lid; it binds only to the assembled 26S proteasome and is positioned close to the ATPase module.The lid scaffold is composed of the Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, and Rpn12 subunits (14). These subunits can be grouped according to their domain structures. Rpn3, Rpn5, Rpn6, Rpn7, Rpn9, and Rpn12 each comprise an N-terminal helix repeat segment, a proteasome-COP9/signalosome-eIF3 (PCI) module, and a long helix at the C terminus (8). The Rpn8 and Rpn11 subunits each consist of an Mpr1–Pad1–N-terminal (MPN) domain, followed by long C-terminal helices (Fig. 1A). The PCI subunits form a horseshoe-shaped structure and the MPN domains form a heterodimer, which are connected by a large helical bundle, to which all subunits contribute (13, 17, 18). Each of these eight subunits has paralogs in the COP9/signalosome (CSN) and the elongation initiation factor 3 (eIF3), which likely adopt a similar architecture (18–21).Open in a separate windowFig. 1.Biochemical activity of the Rpn8-Rpn11 fusion protein. (A) Domain structures of Rpn8, Rpn11 and the fusion protein. (B) Ub₄ cleavage activity of 26S proteasome, WT Rpn8-Rpn11 and Rpn8-Rpn11 (E48Q). Cleavage of labeled peptide from Ub₄ was detected by the change in fluorescence polarization after 1hr incubation at 37 °C at the indicated concentrations. Values are normalized to maximum cleavage activity of 26S proteasome. The used 26S proteasome preparation contained only trace amounts of the DUB Ubp6.The lid strengthens the interaction between the CP and RP (17) and deubiquitylates substrates before their processing by the AAA-ATPase module and the CP. Cleavage of polyubiquitin chains from the substrate enables recycling of Ub into the cellular pool, and the removal of the unfolding-resistant Ub moieties promotes translocation of substrates. The MPN domain of Rpn11 contains the catalytic site for deubiquitylation (22, 23). Rpn11 belongs to the JAB1/MPN/Mov34 metalloenzyme (JAMM) family of metalloproteases, which provide the isopeptidase activities in the proteasome, CSN, and exo-deubiquitylating enzymes (DUBs), such as associated molecule with the SH3 domain of STAM-like protein (AMSH-LP). The signature motif for this family is a conserved glutamate upstream of a zinc-coordinating catalytic loop, H(S/T)HX₇SXXD, first revealed in the structure of an archaeal homolog, AfJAMM (24). The substrate-binding mode of JAMM DUBs was clarified by the crystal structure of AMSH-LP in complex with Lys63-linked diubiquitin (25). The other proteasomal MPN subunit, Rpn8, is catalytically inactive; it does not contain the JAMM motif and appears to have mainly a supporting role for Rpn11. Isolated Rpn11 is catalytically inactive, as is the isolated lid (22). Rpn11 is activated upon integration into the 26S holocomplex and is dependent on ATP hydrolysis (23). The 26S proteasome was recently shown to undergo large-scale conformational changes from a substrate-accepting conformation to a substrate-engaged conformation that may be critical for Rpn11 function (15, 26), but the mechanistic basis for the regulation of Rpn11 remains unclear. Loss-of-function mutants of the JAMM motif cause stalling of substrates above the mouth of the ATPase module and lead to clogging of the 26S proteasome (23, 26).Inhibitors of human Rpn11 (hRpn11, also known as POH1) have been proposed as potential antitumor agents working upstream of the β5 proteolytic subunits in the UPS. The β5 subunits have been clinically validated by the approval of bortezomib and carilfzomib for the treatment of hematologic malignancies. siRNA and mutagenesis studies show that expression of the zinc catalytic domain of hRpn11 is essential for cell survival (27). Inhibition of hRpn11 in combination with EGFR inhibition has been suggested to be beneficial in the treatment of nonsmall cell lung cancer (28). Overexpression of hRpn11 in cancer cells has been linked to their tumor escape from cytotoxic agents (29). Thus, hRpn11 is an attractive target for pharmacologic intervention of the UPS.Here we present three crystal structures of the catalytically active Rpn8/Rpn11 MPN heterodimer from Saccharomyces cerevisiae, revealing the details of the Rpn11 active site and the mode of interaction with other subunits. Not all structures show proper active site geometry, hinting at possible mechanisms preventing activation outside of the proteasome complex. The access path for the C-terminal peptide of the substrate-bound Ub is blocked by a highly conserved insertion specific to Rpn11. Fitting of the Rpn8-Rpn11 crystal structure into the cryo-EM density of both the substrate-accepting and substrate-engaged proteasome revealed how the subcomplex is situated between base and PCI domain subunits, which involves long insertions unique to Rpn11 and Rpn8. Contacts to the coiled coils and the oligosaccharide-binding fold (OB) domain ring of the AAA subunits appear to control active site geometry and proper access of the isopeptide bond segment. In the substrate-engaged proteasome, the catalytic center becomes situated just above the maw of the ATPase ring.     

Use of a curved-array transducer to reduce interobserver variation in sonographic measurement of thyroid volume in healthy adults

PURPOSE: Sonographic calculation of thyroid volume is used in the diagnosis and follow-up of thyroid diseases. Since the calculated volume of thyroid lobes is highly influenced by the longest (ie, craniocaudal) diameter, we examined whether using a curved-array transducer as opposed to a linear-array transducer to measure the craniocaudal diameter would reduce interobserver variation. METHODS: Three sonographers with different levels of expertise each used a 5-12-MHz linear-array transducer and a 2-5-MHz curved-array transducer to measure the craniocaudal diameter of both thyroid lobes of 25 healthy volunteers. On the basis of these measurements, thyroid lobe volumes were calculated. Single-factor analysis of variance was used to evaluate the interobserver variations between the measurements made by all 3 observers as well as between measurements taken by pairs of observers. A p value of less than 0.05 was considered significant. RESULTS: Using the linear-array transducer to measure the craniocaudal diameter resulted in significant interobserver variation in thyroid volume calculation (p = 0.02), whereas using the convex-array transducer did not. Using either transducer resulted in a highly significant interobserver variation in measurements of the craniocaudal diameter, although the variation was far more pronounced for measurements made with the linear-array transducer (p = 0.0005) than for those made with the curved-array transducer (p = 0.04). For both transducers, the interobserver variations were most pronounced between the most and the least experienced sonographers. CONCLUSIONS: To avoid significant interobserver variation in calculating thyroid lobe volume, we recommend using a curved-array transducer to measure the craniocaudal diameter of the thyroid lobes.     

Impact of several histopathological prognosticators and local tumour extension on oncological outcome in pT3b/c N0M0 renal cell carcinoma

OBJECTIVE

To investigate the prognostic relevance of different histopathological features and local tumour extension in patients with pT3b/c N0M0 renal cell carcinoma (RCC), as recently new proposals of reclassifying tumour fat invasion in pT3b/c RCC have been made but the effect of other histopathological tumour characteristics and combinations thereof with tumour invasion has yet to be determined in these patients.

PATIENTS AND METHODS

Between 1990 and 2006, 1943 patients underwent surgical treatment for renal tumours in our institution, of which 175 patients (8.7%) had pT3b/c RCC. After exclusion of 57 patients (32.6%) with lymph node and/or distant metastases at the time of diagnosis, 118 (67.4%) remained for retrospective analysis. Different histopathological features and local tumour extension were studied for their association with cancer‐specific‐survival (CSS) and progression‐free‐survival (PFS) by univariate and multivariate analyses. Histopathology was reviewed and revised according to the 2002 Tumour‐Nodes‐Metastasis (TNM) classification system by one pathologist (S.B.). CSS and PFS were estimated by the Kaplan–Meier method.

RESULTS

Follow‐up data were obtained from 110 patients at a median (range) of 3.2 (0.3–16.1) years. In univariate analysis, microvascular invasion (MVI) and capsular invasion increased the risk of tumour progression by 2.05‐ and 2.72‐times (P = 0.037 and P < 0.001). Overall, tumour fat invasion (TFI) and the presence of areas composed by cells with eosinophilic cytoplasm were associated with a higher risk of progression (P = 0.001 and P = 0.011) and reduced CSS (P = 0.037 and P = 0.017). In multivariate analysis, MVI and capsular invasion were associated with a two‐fold increased risk of dying from cancer (hazard risk ratio, HR 2.22, P = 0.045 and HR 2.31, P = 0.011). TFI in general (P = 0.004) and specifically coexistent perirenal fat invasion (PFI) and renal sinus fat invasion (RSFI) were associated with a three‐fold increased risk of developing tumour progression (HR 3.36, P = 0.001). The 10‐year CSS and PFS rates were 39% and 36% for all patients, 47% and 45% for pT3b/c RCC with no PFI or RSFI, and 25% and 10% for PFI + RSFI.

CONCLUSION

Patients with pT3b/c RCC with MVI, capsular invasion, TFI and especially PFI + RSFI, have a markedly reduced prognosis compared with patients with pT3b/c RCC without these features. When these results are corroborated by additional studies and external validation, modification of the TNM classification system would be a sensible consequence.     

Metabolic and secretory properties of peripheral and synovial granulocytes in rheumatoid arthritis

The metabolic and secretory properties of peripheral and synovial granulocytes of patients with rheumatoid arthritis were investigated with serum- or immunoglobulin-treated zymosan as activators of cell metabolism. During isolation of the synovial cells precautions were taken to prevent in vitro phagocytosis of immune materials present in the synovial fluids. Oxygen uptake, extracellular release of lysosomal enzymes under resting and activated conditions, yield of the isolated granulocytes, and the granule enzyme content of peripheral and synovial cells did not differ significantly from those of peripheral granulocytes from healthy volunteers. In agreement with the biochemical results, intracellular inclusions could be detected in only a few synovial cells with a direct immunofluorescence technique. The possibility that formation of “ragocytes” may be an in vitro phenomenon is discussed.     

Heterogeneity of proteoglycans extracted before and after collagenase treatment of human articular cartilage: I. Physical properties related to age

Proteoglycans were isolated from young and mature human articular cartilage 4 different ways: by direct extraction with 4M guanidine hydrochloride (GuHCl); after digestion of the residue from this first extraction with collagenase, by extraction with 4M GuHCl; associatively with 0.5M GuHCl after digestion of the cartilage with collagenase; and dissociatively with 4M GuHCl after digestion of the cartilage with collagenase. The structural properties of these proteoglycans were compared. Proteoglycan aggregates and monomers isolated from second extractions and from young cartilage were of larger hydrodynamic size than proteoglycans isolated from first extractions and mature cartilage, respectively. The same applied to the chondroitin sulfate chain lengths of these proteoglycans. The proteoglycan fraction from second extractions of cartilage contained a larger proportion of monomers than the fraction from first extractions. Associative extraction of mature collagenase-digested cartilage yielded mainly proteoglycan monomers, whereas an appreciable amount of proteoglycan aggregate was also liberated from young collagenase-digested cartilage. Our results indicate that, because of their larger size, proteoglycans from second extractions of cartilage are more entrapped in the collagen network. These large proteoglycans can only be liberated from the matrix after extraction of the smaller proteoglycans, followed by digestion of the residue with collagenase. This indicates that proteoglycans overlap and entangle with the collagen and protect it from degradation by collagenase.     

Transmaternal cell flow leads to antigen-experienced cord blood

Umbilical cord blood (UCB) is used for HSCT. It is known that UCB can comprise Ag-specific T cells. Here we question whether solely transmaternal cell flow may immunize UCB. Twenty-three female UCB samples were collected from healthy mothers and analyzed for minor histocompatibility Ag HY-specific responses. Forty-two of 104 tetramer(pos) T-cell clones, isolated from 16 of 17 UCB samples, showed male-specific lysis in vitro. Male microchimerism was present in 6 of 12 UCB samples analyzed. In conclusion, female UCB comprises HY-specific cytotoxic T cells. The immunization is presumably caused by transmaternal cell flow of male microchimerism present in the mother. The presence of immune cells in UCB that are not directed against maternal foreign Ags is remarkable and may explain the reported clinical observation of improved HSCT outcome with younger sibling donors.