Telomerase-associated Protein 1, HSP90, and Topoisomerase II�� Associate Directly with the BLM Helicase in Immortalized Cells Using ALT and Modulate Its Helicase Activity Using Telomeric DNA Substrates

The BLM helicase associates with the telomere structural proteins TRF1 and TRF2 in immortalized cells using the alternative lengthening of telomere (ALT) pathways. This work focuses on identifying protein partners of BLM in cells using ALT. Mass spectrometry and immunoprecipitation techniques have identified three proteins that bind directly to BLM and TRF2 in ALT cells: telomerase-associated protein 1 (TEP1), heat shock protein 90 (HSP90), and topoisomerase IIα (TOPOIIα). BLM predominantly co-localizes with these proteins in foci actively synthesizing DNA during late S and G₂/M phases of the cell cycle when ALT is thought to occur. Immunoprecipitation studies also indicate that only HSP90 and TOPOIIα are components of a specific complex containing BLM, TRF1, and TRF2 but that this complex does not include TEP1. TEP1, TOPOIIα, and HSP90 interact directly with BLM in vitro and modulate its helicase activity on telomere-like DNA substrates but not on non-telomeric substrates. Initial studies suggest that knockdown of BLM in ALT cells reduces average telomere length but does not do so in cells using telomerase.Bloom syndrome (BS)⁴ is a genetic disease caused by mutation of both copies of the human BLM gene. It is characterized by sun sensitivity, small stature, immunodeficiency, male infertility, and an increased susceptibility to cancer of all sites and types. The high incidence of spontaneous chromosome breakage and other unique chromosomal anomalies in cells from BS patients indicate an increase in homologous recombination in somatic cells (1). Another notable feature of non-immortalized and immortalized cells from BS individuals is the presence of telomeric associations (TAs) between homologous chromosomes (2). Work from our group and others have suggested a role for BLM in recombination-mediated mechanisms of telomere elongation or ALT (alternative lengthening of telomeres), processes that maintain/elongate telomeres in the absence of telomerase (3–5). However, the exact mechanism by which BLM contributes to telomere stability is unknown.Several proteins interact with and regulate BLM helicase activity, including two telomere-specific proteins, TRF1 and TRF2 (6, 7). Although TRF2 stimulates BLM unwinding of telomeric and non-telomeric 3′-overhang substrates, TRF1 inhibits BLM unwinding of telomeric substrates. TRF2-mediated stimulation of BLM helicase activity on a telomeric substrate is observed when TRF2 is present in excess or with equimolar amount of TRF1 but not when TRF1 is present in molar excess. Both proteins associate with BLM specifically in ALT cells in vivo, suggesting their involvement in the ALT pathways. In addition to TRF1 and TRF2, the telomere single-strand DNA-binding protein POT1 strongly stimulates BLM helicase activity on long telomeric forked duplexes and D-loop structures (8). Other proteins also play an important role in telomere maintenance in telomerase-negative cells, including RAD50, NBS1, and MRE11, which co-localize with TRF1 and TRF2 in specialized ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs) (9–11). Thus, we hypothesize that BLM complex formation may be essential for the ALT mechanism, and its modification may occur dynamically during the specific nucleic acid transactions required to protect the telomere in cells using the ALT pathways.This study has identified previously unknown protein partners of BLM and TRF2 in ALT cells using double immunoprecipitation and mass spectrometry (MS). These include telomerase-associated protein 1 (TEP1), heat shock protein 90 (HSP90), and topoisomerase IIα (TOPOIIα). These proteins associate with BLM and TRF2 in cells using ALT but not in cells using telomerase and directly interact with BLM in vitro. This complex of proteins localizes to sites of new DNA synthesis in vivo in ALT cells, suggesting a role in telomere maintenance. We also identified HSP90 and TOPOIIα in another ALT-specific complex consisting of BLM, TRF1, and TRF2 but not TEP1. In vitro analyses demonstrate that HSP90 inhibits BLM helicase activity using both telomeric and non-telomeric substrates, whereas TEP1 and TOPOIIα initially slow the kinetics of BLM unwinding only using telomeric substrates. These findings suggest the presence of dynamic BLM-associated ALT complexes that include previously unidentified interacting proteins. The function of TEP1 in the BLM·TRF2 complex remains unclear, although its previously described interaction with the RNA subunit of telomerase (12) suggests an interesting hypothesis of cross-talk between mechanisms of telomere elongation.     

PR55��, a Regulatory Subunit of PP2A, Specifically Regulates PP2A-mediated ��-Catenin Dephosphorylation

A central question in Wnt signaling is the regulation of β-catenin phosphorylation and degradation. Multiple kinases, including CKIα and GSK3, are involved in β-catenin phosphorylation. Protein phosphatases such as PP2A and PP1 have been implicated in the regulation of β-catenin. However, which phosphatase dephosphorylates β-catenin in vivo and how the specificity of β-catenin dephosphorylation is regulated are not clear. In this study, we show that PP2A regulates β-catenin phosphorylation and degradation in vivo. We demonstrate that PP2A is required for Wnt/β-catenin signaling in Drosophila. Moreover, we have identified PR55α as the regulatory subunit of PP2A that controls β-catenin phosphorylation and degradation. PR55α, but not the catalytic subunit, PP2Ac, directly interacts with β-catenin. RNA interference knockdown of PR55α elevates β-catenin phosphorylation and decreases Wnt signaling, whereas overexpressing PR55α enhances Wnt signaling. Taken together, our results suggest that PR55α specifically regulates PP2A-mediated β-catenin dephosphorylation and plays an essential role in Wnt signaling.Wnt/β-catenin signaling plays essential roles in development and tumorigenesis (1–3). Our previous work found that β-catenin is sequentially phosphorylated by CKIα⁴ and GSK3 (4), which creates a binding site for β-Trcp (5), leading to degradation via the ubiquitination/proteasome machinery (3). Mutations in β-catenin or APC genes that prevent β-catenin phosphorylation or ubiquitination/degradation lead ultimately to cancer (1, 2).In addition to the involvement of kinases, protein phosphatases, such as PP1, PP2A, and PP2C, are also implicated in Wnt/β-catenin regulation. PP2C and PP1 may regulate dephosphorylation of Axin and play positive roles in Wnt signaling (6, 7). PP2A is a multisubunit enzyme (8–10); it has been reported to play either positive or negative roles in Wnt signaling likely by targeting different components (11–21). Toward the goal of understanding the mechanism of β-catenin phosphorylation, we carried out siRNA screening targeting several major phosphatases, in which we found that PP2A dephosphorylates β-catenin. This is consistent with a recent study where PP2A is shown to dephosphorylate β-catenin in a cell-free system (18).PP2A consists of a catalytic subunit (PP2Ac), a structure subunit (PR65/A), and variable regulatory B subunits (PR/B, PR/B′, PR/B″, or PR/B‴). The substrate specificity of PP2A is thought to be determined by its B subunit (9). By siRNA screening, we further identified that PR55α, a regulatory subunit of PP2A, specifically regulates β-catenin phosphorylation and degradation. Mechanistically, we found that PR55α directly interacts with β-catenin and regulates PP2A-mediated β-catenin dephosphorylation in Wnt signaling.     

Functional Cross-talk between ��-Catenin and NF��B Signaling Pathways in Colonic Crypts of Mice in Response to Progastrin

We recently reported a critical role of NFκB in mediating hyperproliferative and anti-apoptotic effects of progastrin on proximal colonic crypts of transgenic mice overexpressing progastrin (Fabp-PG mice). We now report activation of β-catenin in colonic crypts of mice in response to chronic (Fabp-PG mice) and acute (wild type FVB/N mice) progastrin stimulation. Significant increases were measured in relative levels of cellular and nuclear β-catenin and pβ-cat⁴⁵ in proximal colonic crypts of Fabp-PG mice compared with that in wild type littermates. Distal colonic crypts were less responsive. Interestingly, β-catenin activation was downstream of IKKα,β/NFκB, because treatment of Fabp-PG mice with the NFκB essential modulator (NEMO) peptide (inhibitor of IKKα,β/NFκB activation) significantly blocked increases in cellular/nuclear levels of total β-catenin/pβ-cat⁴⁵/and pβ-cat⁵⁵² in proximal colons. Cellular levels of pβ-cat^33,37,41, however, increased in proximal colons in response to NEMO, probably because of a significant increase in pGSK-3β^Tyr216, facilitating degradation of β-catenin. NEMO peptide significantly blocked increases in cyclin D1 expression, thereby, abrogating hyperplasia of proximal crypts. Goblet cell hyperplasia in colonic crypts of Fabp-PG mice was abrogated by NEMO treatment, suggesting a cross-talk between the NFκB/β-catenin and Notch pathways. Cellular proliferation and crypt lengths increased significantly in proximal but not distal crypts of FVB/N mice injected with 1 nm progastrin associated with a significant increase in cellular/nuclear levels of total β-catenin and cyclin D1. Thus, intracellular signals, activated in response to acute and chronic stimulation with progastrin, were similar and specific to proximal colons. Our studies suggest a novel possibility that activation of β-catenin, downstream to the IKKα,β/NFκB pathway, may be integral to the hyperproliferative effects of progastrin on proximal colonic crypts.Accumulating evidence suggests that gastrins play an important role in proliferation and carcinogenesis of gastrointestinal and pancreatic cancers (1, 2). Progastrin and glycine-extended gastrin (G-Gly)³ are predominant forms of gastrins found in many tumors, including colon (3–5). Progastrin exerts potent proliferative and anti-apoptotic effects in vitro and in vivo on intestinal mucosal cells (6–10) and on pancreatic cancer cells (11). Transgenic mice overexpressing progastrin from either the liver (hGAS) or intestinal epithelial cells (Fabp-PG) are at a higher risk for developing pre-neoplastic and neoplastic lesions in colons in response to azoxymethane (12–15). Treatment with G-Gly similarly increased the risk for developing pre-neoplastic lesions in rats (16). Thus progastrin and G-Gly exert co-carcinogenic effects in vivo (12–16).Under physiological conditions, only processed forms of gastrins (G17, G34) are present in the circulation (17). In certain disease states, elevated levels of circulating progastrin (0.1 to >1.0 nm) are measured (1). Because co-carcinogenic effects of progastrin are measured in Fabp-PG mice, which express pathophysiological concentrations of hProgastrin (<1–5 nm) (12), elevated levels of circulating progastrin measured in certain disease states in humans may play a role in colon carcinogenesis. A curious finding was that pre-neoplastic and neoplastic lesions were significantly increased in proximal, but not distal, colons of Fabp-PG mice, in response to azoxymethane (12, 14), which may reflect an increase in proliferation and a decrease in azoxymethane-induced apoptosis in proximal colons of Fabp-PG mice (18). We reported a critical role of NFκB activation in mediating proliferation and the anti-apoptotic effect of progastrin on pancreatic cancer cells (in vitro) and on proximal colonic crypts of Fabp-PG mice (in vivo) (11, 18). Whereas the Wnt/β-catenin pathway is known to play a role in the proliferation of colonic crypts (19), its role in mediating biological effects of progastrin remains unknown.β-Catenin is regulated by canonical (GSK-3β phosphorylation-dependent) and non-canonical (GSK-3β phosphorylation-independent) pathways. In the canonical pathway, inhibition of GSK-3β protects β-catenin against degradation by protein complexes, consisting of GSK-3β, axin, and adenomatous polyposis coli (20). In a resting cell, β-catenin is not present in the cytoplasm or nucleus because of proteasomal degradation of β-catenin that is not bound to E-cadherin (20). Following inactivation of GSK-3β, β-catenin stabilizes in the cytoplasm and translocates to the nucleus where it cooperates with Tcf/Lef for activation of target genes (20). In the current studies, we examined whether β-catenin is activated in proximal versus distal colonic crypts of Fabp-PG mice. Relative levels of β-catenin and its target gene product, cyclin D1, were significantly increased in proximal versus distal colonic crypts of Fabp-PG mice. We next examined a possible cross-talk between NFκB and β-catenin activation and the role of GSK-3β. Our results suggest the novel possibility that β-catenin activation in response to progastrin is downstream to IKKα,β/NFκB p65 activation, and that phosphorylation of GSK-3β at Tyr²¹⁶ may be critically involved.To examine whether differences measured in the response of proximal versus distal colons in Fabp-PG mice were not an artifact of chronic stimulation, we additionally injected WT FVB/N mice with progastrin, as an acute model of stimulation. Our results confirmed that differences we had measured in Fabp-PG mice are not an artifact of chronic stimulation but represent inherent differences in the response of proximal versus distal colonic crypts to circulating progastrins.We and others (18, 21) have previously demonstrated goblet cell hyperplasia in colonic crypts of transgenic mice overexpressing progastrin. In the current studies, we confirmed a significant increase in goblet cell hyperplasia/metaplasia (?) in proximal colonic crypts of Fabp-PG mice. Importantly, goblet cell hyperplasia was reversed to wild type levels by attenuating NFκB activation (and hence β-catenin activation) in NEMO-treated mice. The results of the current studies thus further suggest that pathways which dictate goblet cell lineage may be modulated by progastrin and may be downstream of NFκB/β-catenin activation. This represents a novel paradigm, which needs to be further examined.     

A ��-l-Arabinopyranosidase from Streptomyces avermitilis Is a Novel Member of Glycoside Hydrolase Family 27

Arabinogalactan proteins (AGPs) are a family of plant cell surface proteoglycans and are considered to be involved in plant growth and development. Because AGPs are very complex molecules, glycoside hydrolases capable of degrading AGPs are powerful tools for analyses of the AGPs. We previously reported such enzymes from Streptomyces avermitilis. Recently, a β-l-arabinopyranosidase was purified from the culture supernatant of the bacterium, and its corresponding gene was identified. The primary structure of the protein revealed that the catalytic module was highly similar to that of glycoside hydrolase family 27 (GH27) α-d-galactosidases. The recombinant protein was successfully expressed as a secreted 64-kDa protein using a Streptomyces expression system. The specific activity toward p-nitrophenyl-β-l-arabinopyranoside was 18 μmol of arabinose/min/mg, which was 67 times higher than that toward p- nitrophenyl-α-d-galactopyranoside. The enzyme could remove 0.1 and 45% l-arabinose from gum arabic or larch arabinogalactan, respectively. X-ray crystallographic analysis reveals that the protein had a GH27 catalytic domain, an antiparallel β-domain containing Greek key motifs, another antiparallel β-domain forming a jellyroll structure, and a carbohydrate-binding module family 13 domain. Comparison of the structure of this protein with that of α-d-galactosidase showed a single amino acid substitution (aspartic acid to glutamic acid) in the catalytic pocket of β-l-arabinopyranosidase, and a space for the hydroxymethyl group on the C-5 carbon of d-galactose bound to α-galactosidase was changed in β-l-arabinopyranosidase. Mutagenesis study revealed that the residue is critical for modulating the enzyme activity. This is the first report in which β-l-arabinopyranosidase is classified as a new member of the GH27 family.Arabinogalactan proteins (AGPs)³ are a family of complex proteoglycans widely distributed in plants (1, 2). AGPs are also found in tree exudate gums and coniferous woods (3) and are characterized by the presence of large amounts of carbohydrate components rich in galactose (all the sugars in the present study are in the d-configuration unless otherwise specified) and l-arabinose and by protein components rich in hydroxyproline, serine, threonine, alanine, and glycine (4). Type II arabinogalactans and short oligosaccharides are the two types of carbohydrates attached to the AGP backbone. Type II arabinogalactans have β-1,3-linked galactosyl backbones in mono- or oligo-β-1,6-galactosyl and/or l-arabinosyl side chains (2, 5). l-Arabinose and lesser amounts of other auxiliary sugars such as glucuronic acid, l-rhamnose, and l-fucose are attached to the side chains primarily at nonreducing termini (2). Molecular and biochemical evidence indicates that AGPs have specific functions during root formation, promotion of somatic embryogenesis, and attraction of pollen tubes to the style (6). However, because many putative protein cores exist and the structures of the carbohydrate moieties are complex, it has been difficult to differentiate one AGP species from another in plant tissues. This, in turn, has made it difficult to assign specific roles to individual AGPs. Despite significant physiological interest in AGPs, there are few studies on glycoside hydrolases that cleave the sugar moieties of these proteins. It is important to study such enzymes because hydrolytic enzymes specific to particular sugar residues or to a type of glycosidic linkage would be useful tools in the structural analysis of AGPs.So far, we have focused on the β-1,3-β-1,6-galactan backbone, which is the common structure of heterogeneous AGPs, to identify glycoside hydrolases acting on AGPs. Galactanases that hydrolyze β-1,3- or β-1,6-galactosyl linkages are useful tools because the enzymes hydrolyze AGPs and produce the constituent carbohydrate moieties of AGPs. We cloned two kinds of galactanases: exo-β-1,3-galactanase (EC 3.2.1.145) from Phanerochaete chrysosporium and endo-β-1,6-galactanase (EC 3.2.1.164) from Trichoderma viride, and demonstrated that the enzymes were novel and could be classified as glycoside hydrolase family 43 (GH43) and family 5 (GH5), respectively (7–9) (see the CAZy website). Genes encoding proteins similar to such enzymes were also identified in the Streptomyces avermitilis genome (10, 11).Because S. avermitilis has two different kinds of galactanases, we focused on finding novel AGP-degrading enzymes. We have cultivated the actinomycete using gum arabic as a carbon source, and isolated a novel β-l-arabinopyranosidase. To the best of our knowledge, the only report on β-l-arabinosidase (EC 3.2.1.88) has been on its purification from Cajanus indicus (12). The amino acid composition of the enzyme was investigated (13), but its sequence remains unknown. In this article, we cloned β-l-arabinopyranosidase from S. avermitilis (SaArap27A), analyzed its catalytic properties, and analyzed the crystal structure of the recombinant enzyme. The results clearly showed that this enzyme is β-l-arabinopyranosidase and is a novel member of the glycoside hydrolase family 27 (GH27). This is the first detailed report on β-l-arabinopyranosidase.     

The Elucidation of the Structure of Thermotoga maritima Peptidoglycan Reveals Two Novel Types of Cross-link

Thermotoga maritima is a Gram-negative, hyperthermophilic bacterium whose peptidoglycan contains comparable amounts of l- and d-lysine. We have determined the fine structure of this cell-wall polymer. The muropeptides resulting from the digestion of peptidoglycan by mutanolysin were separated by high-performance liquid chromatography and identified by amino acid analysis after acid hydrolysis, dinitrophenylation, enzymatic determination of the configuration of the chiral amino acids, and mass spectrometry. The high-performance liquid chromatography profile contained four main peaks, two monomers, and two dimers, plus a few minor peaks corresponding to anhydro forms. The first monomer was the d-lysine-containing disaccharide-tripeptide in which the d-Glu-d-Lys bond had the unusual γ→ϵ arrangement (GlcNAc-MurNAc-l-Ala-γ-d-Glu-ϵ-d-Lys). The second monomer was the conventional disaccharide-tetrapeptide (GlcNAc-MurNAc-l-Ala-γ-d-Glu-l-Lys-d-Ala). The first dimer contained a disaccharide-l-Ala as the acyl donor cross-linked to the α-amine of d-Lys in a tripeptide acceptor stem with the sequence of the first monomer. In the second dimer, donor and acceptor stems with the sequences of the second and first monomers, respectively, were connected by a d-Ala⁴-α-d-Lys³ cross-link. The cross-linking index was 10 with an average chain length of 30 disaccharide units. The structure of the peptidoglycan of T. maritima revealed for the first time the key role of d-Lys in peptidoglycan synthesis, both as a surrogate of l-Lys or meso-diaminopimelic acid at the third position of peptide stems and in the formation of novel cross-links of the l-Ala¹(α→α)d-Lys³ and d-Ala⁴(α→α)d-Lys³ types.Peptidoglycan (or murein) is a giant macromolecule whose main function is the protection of the cytoplasmic membrane against the internal osmotic pressure. It is composed of alternating residues of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc)² cross-linked by short peptides (1). The composition of the peptide stem in nascent peptidoglycan is l-Ala¹-γ-d-Glu²-X³-d-Ala⁴-d-Ala⁵, where X is most often meso-diaminopimelic acid (meso-A₂pm) or l-lysine in Gram-negative and Gram-positive species, respectively (2, 3). In the mature macromolecule, the last d-Ala residue is removed. Cross-linking of the glycan chains generally occurs between the carboxyl group of d-Ala at position 4 of a donor peptide stem and the side-chain amino group of the diamino acid at position 3 of an acceptor peptide stem (4→3 cross-links). Cross-linking is either direct or through a short peptide bridge such as pentaglycine in Staphylococcus aureus (2, 3). The enzymes for the formation of the 4→3 cross-links are active-site serine dd- transpeptidases that belong to the penicillin-binding protein (PBP) family and are the essential targets of β-lactam antibiotics in pathogenic bacteria (4). Catalysis involves the cleavage of the d-Ala⁴-d-Ala⁵ bond of a donor peptide stem and the formation of an amide bond between the carboxyl of d-Ala⁴ and the side chain amine at the third position of an acceptor stem. Transpeptidases of the ld specificity are active-site cysteine enzymes that were shown to act as surrogates of the PBPs in mutants of Enterococcus faecium resistant to β-lactam antibiotics (5). They cleave the X³-d-Ala⁴ bond of a donor stem peptide to form 3→3 cross-links. This alternate mode of cross-linking is usually marginal, although it has recently been shown to predominate in non-replicative “dormant” forms of Mycobacterium tuberculosis (6).Thermotoga maritima is a Gram-negative, extremely thermophilic bacterium isolated from geothermally heated sea floors by Huber et al. (7). A morphological characteristic is the presence of an outer sheath-like envelope called “toga.” Although the organism has received considerable attention for its biotechnological potential, studies about its peptidoglycan are scarce (8–11), and in particular the fine structure of the macromolecule is still unknown. In their initial work, Huber et al. (7) showed that the composition of its peptidoglycan was unusual for a Gram-negative species, because it contained both isomers of lysine and no A₂pm. Recently, we purified and studied the properties of T. maritima MurE (12); this enzyme is responsible for the addition of the amino acid residue at position 3 of the peptide stem (13, 14). We demonstrated that T. maritima MurE added in vitro l- and d-Lys to UDP-MurNAc-l-Ala-d-Glu. Although l-Lys was added in the usual way, yielding the conventional nucleotide UDP-MurNAc-l-Ala-γ-d-Glu-l-Lys containing a d-Glu(γ→α)l-Lys amide bond, the d-isomer was added in an “upside-down” manner, yielding the novel nucleotide UDP-MurNAc-l-Ala-d-Glu(γ→ϵ)d-Lys. We also showed that the d-Lys-containing nucleotide was not a substrate for T. maritima MurF, the subsequent enzyme in the biosynthetic pathway, whereas this ligase catalyzed the addition of dipeptide d-Ala-d-Ala to the l-Lys-containing tripeptide, yielding the conventional UDP-MurNAc-pentapeptide (12).However, both the l-Lys-containing UDP-MurNAc-pentapeptide and d-Lys-containing UDP-MurNAc-tripeptide were used as substrates by T. maritima MraY with comparable efficiencies in vitro (12). This observation implies that the unusual d-Lys-containing peptide stems are likely to be translocated to the periplasmic face of the cytoplasmic membrane and to participate in peptidoglycan polymerization. Therefore, we have determined here the fine structure of T. maritima peptidoglycan and we have shown that l-Lys- and d-Lys-containing peptide stems are both present in the polymer, the latter being involved in the formation of two novel types of peptidoglycan cross-link.     

The structural diversity in α1-antitrypsin misfolding

The structure of α1-antitrypsin polymers, which cause a devastating disease, is vigorously debated. Here, the state of the field is discussed in view of a paradigm-changing structure published in this issue of EMBO reports.EMBO Rep (2011) advance online publication. doi:10.1038/embor.2011.171We were all taught that proteins have to fold correctly to be active and that the primary sequence of amino acids acts as the ‘blueprint'' for successful, productive folding. In recent years, we have also learnt how sensitive that blueprint is to change. For example, a single amino-acid change in the protein sequence, or a subtle change in temperature at which folding takes place, can lead to the formation and accumulation of non-native species, which have a tendency to self-associate and deposit in and around tissues, thereby triggering disease. To understand protein misfolding and its links with disease, we need information about the structures of all the key players and their relationships with each other. This has proven exceptionally challenging due to the transient nature of many of the species involved and the heterogeneity of the final misfolded product.For one misfolding disorder, α₁-antitrypsin deficiency—a devastating disease that affects approximately 1 in 2,500 individuals—we are a step closer to characterizing all of the main culprits. In this issue of EMBO reports, Huntington and colleagues present the X-ray crystal structure of an α₁-antitrypsin trimer that sheds light on the structure of a potentially pathogenic form of α₁-antitrypsin and provides new insights into the molecular mechanism of α₁-antitrypsin deficiency (Yamasaki et al, 2011).Attempts to understand the molecular basis for α₁-antitrypsin deficiency began in 1963 when Laurell & Eriksson noticed its absence from the serum of a cohort of patients with obstructive lung disease (Laurell & Eriksson, 1963). Sharp and co-workers subsequently described periodic acid Schiff-positive inclusions of α₁-antitrypsin within hepatocytes of α₁-antitrypsin-deficient patients (Sharp et al, 1969). These two findings linked the major clinical outcomes of the disease. α₁-Antitrypsin inhibits elastase in the lower respiratory tract and, therefore, a plasma deficiency leads to early onset emphysema due to uncontrolled elastase activity. The aggregation of α₁-antitrypsin at its site of production—the hepatocyte—leads to liver damage and cirrhosis. In the early 1990s, elegant work by Lomas and colleagues revealed that the key molecular event leading to the deficiency was the misfolding and formation of α₁-antitrypsin polymers within the endoplasmic reticulum of hepatocytes (Lomas et al, 1992).α₁-Antitrypsin, like all members of the serpin superfamily, is a large single-domain protein consisting of 394 amino acids that fold into three β-sheets surrounded by nine α-helices (Fig 1; Elliott et al, 2000). Protruding from the core structure is the flexible reactive centre loop, containing the scissile bond that dictates the inhibitory specificity of a serpin. Similar to all serpins, α₁-antitrypsin undergoes a marked conformational change to inhibit proteinases, which involves the insertion of the reactive centre loop into the middle of β-sheet A. This conformational change is possible because the native state of the serpin superfamily is metastable. However, the instability of the native state of α₁-antitrypsin makes it extremely susceptible to misfolding and polymerization, which results in the formation of more thermodynamically stable conformations. The most common mutation that causes polymerization in α₁-antitrypsin is the Z mutation (Glu342Lys), which is present in approximately 4% of northern Europeans. This mutation does not alter the stability of the native molecule but slows down its folding rate such that a polymerization-prone intermediate state persists longer, favouring polymerization (Knaupp et al, 2010). In addition, the native state of Z α₁-antitrypsin is more easily polymerized than its wild-type counterpart (Lomas et al, 1992). Although we have known the structure of native wild-type α₁-antitrypsin for more than 10 years (Elliott et al, 2000), and despite a wealth of biochemical and biophysical studies, we do not know the structure of the final polymeric form.Open in a separate windowFigure 1Structures of native α₁-antitrypsin and the known three types of polymer. The reactive centre loop region is highlighted in blue. Antitrypsin is deposited in the Protein Data Bank, ID no. 1QLP. Models of the s4A/s5A swap polymer and carboxy-terminal swap polymer were kindly provided by Professor J. Huntington; the model of the s4A swap polymer was kindly provided by Professor J. Whisstock.Over the past 20 years, various linkages between α₁-antitrypsin monomers have been reported and/or suggested, which involve different sheets and extents of interaction. Until recently, the most widely accepted model for α₁-antitrypsin polymerization involved the reactive centre loop of one molecule entering the β-sheet A of another in the strand 4 position (s4A swap polymer; Fig 1; Sivasothy et al, 2000), which was supported by extensive biochemical and biophysical analyses. This model was recently challenged when Yamasaki and colleagues described a new polymeric linkage in which monomers were linked by the insertion of two strands (strands 4 and 5) into β-sheet A of another serpin (s4A/s5A swap polymer; Fig 1; Yamasaki et al, 2008). Notably, these polymers were formed in the presence of the denaturant guanidine hydrochloride and so their physiological relevance was unclear. Extensive experimental work by the Lomas group has shown that heat-induced polymerization of α₁-antitrypsin produces polymers with a structure similar to those formed in hepatocellular inclusions (Ekeowa et al, 2010). The key to their studies was the identification and characterization of the antibody 2C1, which recognizes only polymerized α₁-antitrypsin formed both in vitro and in vivo (Miranda et al, 2010).“One of the most striking results of this work is the heterogeneity of polymer formation, which has important implications…”In this current paper, Yamasaki and colleagues set out to determine the structure of these heat-induced polymers. The authors initially compare heat- and denaturant-induced polymers by using native PAGE. They find that the s4A/s5A swap polymers dominate when denaturant is used to induce polymerization, whereas the heat-induced polymers are made up of a mixture of s4A/s5A swap polymers and another polymer morphology that binds to the 2C1 antibody. By using this information, they construct a recombinant α₁-antitrypsin molecule that cannot undergo the s4A/s5A swap reaction. By heating this α₁-antitrypsin variant at 60 °C, they form and subsequently purify short polymers that bind to the 2C1 antibody, indicating that they contain the pathological structure. The resultant polymer is a trimer that cannot be extended. Structural analysis showed that the monomers are linked through a swap of secondary structure involving the carboxyl terminus of the protein, specifically the first strand from the β-sheet C and strands 4 and 5 from β-sheet B were swapped from one serpin to another (C-terminal swap polymer; Fig 1).“…more than one polymer structure might be formed simultaneously during polymerization […] toxic and non-toxic polymers might coexist”The C-terminal swap polymer was obtained by heating recombinant protein at 60 °C, raising questions about its biological relevance, which the authors tried to answer by using protein engineering. For the C-terminal swap polymer to form, the C-terminus must move. Thus, the authors engineered a disulphide bond between the third strand of β-sheet C and the C-terminus, effectively preventing the conformational change. Notably, when this disulphide-bonded protein was polymerized by using heat, only s4A/s5A swap polymers—which cannot bind to the 2C1 antibody—were formed. In further experiments, they used a protein engineering approach to examine what happens in two cell models—the yeast Pichia pastoris and monkey COS-7 cells—of Z α₁-antitrypsin production. Both models produce Z α₁-antitrypsin polymers that react with the 2C1 antibody. By using the introduced cysteine residues to probe for the polymeric linkage, they were able to show that the C-terminal swap mechanism dominated in both cell models.The study by Yamasaki and colleagues provides another important piece of the puzzle in identifying, characterizing and linking all the players involved in α₁-antitrypsin deficiency. One of the most striking results of this work is the heterogeneity of polymer formation, which has important implications for understanding this disease and the development of therapeutic strategies. α₁-Antitrypsin is a flexible molecule capable of extreme conformational change and this inherent ‘desire'' for a more stable conformation makes it susceptible to polymerization. Numerous parallel pathways of polymer production probably occur, but the structural and/or environmental factors involved in deciding which pathway is followed remain unknown. In addition, does this ability to form different polymers affect which type of polymer is cleared from the cell? The kinetics of these polymerization reactions need to be elucidated and previous studies by several groups might need to be re-evaluated, as it is possible that heterogeneous populations of polymers were being formed, which would confuse the data analysis.From a biomedical perspective, identifying the pathological species and determining how it damages the liver is critical. The C-terminal swap polymer is probably found in hepatocytes, but this does not mean that it is the toxic agent. The results of the Yamasaki study suggest that more than one polymer structure might be formed simultaneously during polymerization, which raises the possibility that toxic and non-toxic polymers might coexist. Therefore, another polymer form—such as the s4A/s5A swap polymer or one not yet identified—could be damaging to cells. Answers to these questions will come in time and hopefully will lead to successful therapeutic approaches to prevent α₁-antitrypsin deficiency.     

GSK-3 Phosphorylates ��-Catenin and Negatively Regulates Its Stability via Ubiquitination/Proteosome-mediated Proteolysis

δ-Catenin was first identified because of its interaction with presenilin-1, and its aberrant expression has been reported in various human tumors and in patients with Cri-du-Chat syndrome, a form of mental retardation. However, the mechanism whereby δ-catenin is regulated in cells has not been fully elucidated. We investigated the possibility that glycogen-synthase kinase-3 (GSK-3) phosphorylates δ-catenin and thus affects its stability. Initially, we found that the level of δ-catenin was greater and the half-life of δ-catenin was longer in GSK-3β^−/− fibroblasts than those in GSK-3β^+/+ fibroblasts. Furthermore, four different approaches designed to specifically inhibit GSK-3 activity, i.e. GSK-3-specific chemical inhibitors, Wnt-3a conditioned media, small interfering RNAs, and GSK-3α and -3β kinase dead constructs, consistently showed that the levels of endogenous δ-catenin in CWR22Rv-1 prostate carcinoma cells and primary cortical neurons were increased by inhibiting GSK-3 activity. In addition, it was found that both GSK-3α and -3β interact with and phosphorylate δ-catenin. The phosphorylation of ΔC207-δ-catenin (lacking 207 C-terminal residues) and T1078A δ-catenin by GSK-3 was noticeably reduced compared with that of wild type δ-catenin, and the data from liquid chromatography-tandem mass spectrometry analyses suggest that the Thr¹⁰⁷⁸ residue of δ-catenin is one of the GSK-3 phosphorylation sites. Treatment with MG132 or ALLN, specific inhibitors of proteosome-dependent proteolysis, increased δ-catenin levels and caused an accumulation of ubiquitinated δ-catenin. It was also found that GSK-3 triggers the ubiquitination of δ-catenin. These results suggest that GSK-3 interacts with and phosphorylates δ-catenin and thereby negatively affects its stability by enabling its ubiquitination/proteosome-mediated proteolysis.δ-Catenin was first identified as a molecule that interacts with presenilin-1 (PS-1)² by yeast two-hybrid assay (1) and was found to belong to the p120-catenin subfamily of armadillo proteins, which characteristically contain 10 Arm repeats (2). In addition to its interaction with PS-1 and its abundant expression in brain (3, 4), several lines of evidence indicate that δ-catenin may play a pivotal role in cognitive function. First, the hemizygous loss of δ-catenin is known to be closely correlated with Cri-du-Chat syndrome, a severe form of mental retardation in humans (5). Second, severe learning deficits and abnormal synaptic plasticity were found in δ-catenin-deficient mice (6). Moreover, in δ-catenin^−/− mice, paired pulse facilitation (a form of short term plasticity) was found to be reduced, and long term potentiation, which is related to the forming and storage mechanisms of memory, was deficient (7, 8). Third, δ-catenin interacting molecules, such as PSs (1, 9), cadherins (10), S-SCAM (2), and PSD-95 (11), have been shown to play important roles in modulating synaptic plasticity. However, even though the maintenance of an adequate δ-catenin level is known to be critical for normal brain function, few studies have been undertaken to identify the factors that regulate δ-catenin stability in cells. We have previously demonstrated that PS-1 inhibits δ-catenin-induced cellular branching and promotes δ-catenin processing and turnover (12).Because of structural similarities among β-catenin, p120-catenin, and δ-catenin and to their shared binding partners (i.e. PS-1 (1, 9) and cadherins (10)), glycogen-synthase kinase-3 (GSK-3) drew our attention as a potential candidate effector of δ-catenin stability in cells. GSK-3 is a serine/threonine kinase and has two highly homologous forms, GSK-3α and GSK-3β, in mammals (13). Although GSK-3α and GSK-3β have similar structures, they differ in mass (GSK-3α (51 kDa) and GSK-3β (47 kDa) (13)) and to some extent in function (14). GSK-3 is a well established inhibitor of Wnt signaling. Moreover, it is known to phosphorylate β-catenin, which results in its degradation via ubiquitination/proteosome-dependent proteolysis (15). GSK-3 is ubiquitously distributed in the human body, but it is particularly abundant in brain (13), and it is interesting that δ-catenin is also abundant in the nervous system (4) and that GSK-3 participates in the progression of Alzheimer disease (16). The majority of GSK-3 substrates have the consensus sequence (Ser/Thr)-Xaa-Xaa-Xaa-(Ser/Thr) (17). Interestingly, we found that δ-catenin has several putative phosphorylation sites targeted by GSK-3, which suggests that δ-catenin can be regulated by GSK-3 in the same way as β-catenin.In this report, we demonstrate that both GSK-3α and -3β interact with and phosphorylate δ-catenin and that this leads to its subsequent ubiquitination and degradation via proteosome-dependent proteolysis. Our results strongly suggest that GSK-3 is a key regulator of δ-catenin stability in cells.     

A New Family of Ty1-copia-Like Retrotransposons Originated in the Tomato Genome by a Recent Horizontal Transfer Event

The use of β-lactam antibiotics has led to the evolution and global spread of a variety of resistance mechanisms, including β-lactamases, a group of enzymes that degrade the β-lactam ring. The evolution of increased β-lactam resistance was studied by exposing independent lineages of Salmonella typhimurium to progressive increases in cephalosporin concentration. Each lineage carried a β-lactamase gene (bla_TEM-1) that provided very low resistance. In most lineages, the initial response to selection was an amplification of the bla_TEM-1 gene copy number. Amplification was followed in some lineages by mutations (envZ, cpxA, or nmpC) that reduced expression of the uptake functions, the OmpC, OmpD, and OmpF porins. The initial resistance provided by bla_TEM-1 amplification allowed the population to expand sufficiently to realize rare secondary point mutations. Mathematical modeling showed that amplification often is likely to be the initial response because events that duplicate or further amplify a gene are much more frequent than point mutations. These models show the importance of the population size to appearance of later point mutations. Transient gene amplification is likely to be a common initial mechanism and an intermediate in stable adaptive improvement. If later point mutations (allowed by amplification) provide sufficient adaptive improvement, the amplification may be lost.THE extensive use of β-lactam antibiotics has led to the evolution and spread of many chromosomal-, plasmid-, and transposon-borne resistance mechanisms (Livermore 1995; Weldhagen 2004). Prominent among these mechanisms is a class of enzymes, β-lactamases, that hydrolyze the β-lactam ring (Ambler 1980; Poole 2004). TEM-1 β-lactamase, encoded by the bla_TEM-1 gene, hydrolyzes both penicillins and early cephalosporins (Matagne et al. 1990). As bacteria developed resistance, stable extended-spectrum cephalosporins (ESCs) were introduced, leading to evolution of TEM sequence variants with improved ESC hydrolysis (Petrosino et al. 1998). Resistance to β-lactams can also result from mutations that reduce levels of outer membrane proteins involved in uptake, altered target proteins (penicillin-binding proteins) to reduce β-lactam binding, or increased expression of efflux pumps that export the antibiotics (Poole 2004; Martínez-Martínez 2008; Zapun et al. 2008).Resistance to β-lactam antibiotics is linearly correlated with the lactamase level over a large range (Nordström et al. 1972) and resistance to β-lactam antibiotics can be provided by increasing enzyme levels. An early illustration of this process is the finding that Escherichia coli can develop ampicillin resistance by amplifying its ampC gene (Edlund and Normark 1981). Similar amplification has been observed in both eubacteria and eukaryotes (Craven and Neidle 2007; Wong et al. 2007) in response to various selective pressures, including antibiotics (Andersson and Hughes 2009; Sandegren and Andersson 2009). In an unselected bacterial population, the frequency of cells with a duplication of any specific chromosomal region ranges between 10⁻² and 10⁻⁵ depending on the region (Anderson and Roth 1981), whereas a point mutation in that gene is expected to be carried by perhaps 1 cell in 10⁷–10⁸ (Hudson et al. 2002). Thus, the rate of duplication formation is ∼10⁻⁵/cell/division and further increases ∼0.01/cell/division (Pettersson et al. 2008) while the base substitution rate is ∼10⁻¹⁰/cell/division/base pair (Hudson et al. 2002). Thus, it is apparent that variants with an increased level of any enzyme activity are more likely to owe the increase to a gene copy number change than to a point mutation. Furthermore, because of the high intrinsic instability of tandem amplifications, haploid segregants are expected to take over the population when the selection pressure is released (Pettersson et al. 2008).To examine the importance of gene amplification in bacterial adaptation to cephalosporins, several independent Salmonella typhimurium lineages carrying the bla_TEM-1 gene were allowed to develop resistance to progressively increased concentrations of cephalothin (a first-generation cephalosporin) and cefaclor (a second-generation cephalosporin). As these lineages developed resistance to higher antibiotic levels, amplification of the bla_TEM-1 gene was the primary and most common resistance mechanism, which in some cases was followed by acquisition of rare point mutations that provided stable resistance.     

The Role of Nitric-oxide Synthase in the Regulation of UVB Light-induced Phosphorylation of the �� Subunit of Eukaryotic Initiation Factor 2

UV light induces phosphorylation of the α subunit of the eukaryotic initiation factor 2 (eIF2α) and inhibits global protein synthesis. Both eIF2 kinases, protein kinase-like endoplasmic reticulum kinase (PERK) and general control of nonderepressible protein kinase 2 (GCN2), have been shown to phosphorylate eIF2α in response to UV irradiation. However, the roles of PERK and GCN2 in UV-induced eIF2α phosphorylation are controversial. The one or more upstream signaling pathways that lead to the activation of PERK or GCN2 remain unknown. In this report we provide data showing that both PERK and GCN2 contribute to UV-induced eIF2α phosphorylation in human keratinocyte (HaCaT) and mouse embryonic fibroblast cells. Reduction of expression of PERK or GCN2 by small interfering RNA decreases phosphorylation of eIF2α after UV irradiation. These data also show that nitric-oxide synthase (NOS)-mediated oxidative stress plays a role in regulation of eIF2α phosphorylation upon UV irradiation. Treating the cells with the broad NOS inhibitor N^G-methyl-l-arginine, the free radical scavenger N-acetyl-l-cysteine, or the NOS substrate l-arginine partially inhibits UV-induced eIF2α phosphorylation. The results presented above led us to propose that NOS mediates UV-induced eIF2α phosphorylation by activation of both PERK and GCN2 via oxidative stress and l-arginine starvation signaling pathways.UV irradiation inhibits translation initiation through activation of kinases that phosphorylate the α-subunit of eukaryotic initiation factor 2 (eIF2α).² Two eIF2α kinases, double strand RNA-dependent protein kinase-like ER kinase (PERK) and general control of amino acid biosynthesis kinase (GCN2), are known to phosphorylate the serine 51 of eIF2α in response to UV irradiation (1–4). However, the one or more upstream pathways that activate eIF2α kinase(s) upon UV irradiation are not known. In this report, we provide evidence that UV-induced nitric-oxide synthase (NOS) activation and nitric oxide (NO^•) production regulate both PERK and GCN2 activation upon UVB irradiation.Expression of inducible nitric-oxide synthase in a mouse macrophage cell line leads to the phosphorylation of eIF2α and inhibition of translation (5). In cultured neuronal and pancreatic cell lines, production of NO^• and peroxynitrite (ONOO⁻) induces endoplasmic reticulum (ER) stress, which activates PERK and results in cell dysfunction and apoptosis (6–9). Cytokine-stimulated inducible nitric-oxide synthase activation in astrocytes depletes l-arginine and activates GCN2, which phosphorylates eIF2α (10). UV irradiation also activates NOS and elevates cellular NO^• (11–13). However, the UV-induced NOS activation and NO^• production have never been shown to be related to the activation of eIF2α kinase(s). Now we demonstrate that UV-induced activation of NOS mediates the activation of both PERK and GCN2, which coordinately regulate the phosphorylation of eIF2α.