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BackgroundThe glycosylation pathways of several eukaryotic protein expression hosts are being engineered to enable the production of therapeutic glycoproteins with humanized application-customized glycan structures. In several expression hosts, this has been quite successful, but one caveat is that the new N-glycan structures inadvertently might be substrates for one or more of the multitude of endogenous glycosyltransferases in such heterologous background. This then results in the formation of novel, undesired glycan structures, which often remain insufficiently characterized.ResultsWhen expressing mouse interleukin-22 (mIL-22) in a Pichia pastoris (syn. Komagataella phaffi) GlycoSwitchM5 strain which had been optimized to produce Man5GlcNAc2 N-glycans, glycan profiling revealed two major species: Man5GlcNAc2 and an unexpected, partially α-mannosidase-resistant structure. A detailed structural analysis using exoglycosidase sequencing, mass spectrometry, linkage analysis and NMR, revealed that this novel glycan was Man5GlcNAc2 modified with a Glcα-1,2-Manβ-1,2-Manβ-1,3-Glcα-1,3-R tetra-saccharide. Also the biosynthetic intermediates of this off-target modification were detected. Expression of a Golgi-targeted GlcNAc Transferase-I strongly inhibited the formation of this novel modification, resulting in more homogeneous modification with the targeted GlcNAcMan5GlcNAc2 structure. We have also observed the off-target glycan on other glycoproteins produced in the GlycoSwitchM5 strain. This illustrates the intricacies of Golgi glycosylation pathways and cautions that the use of glyco-engineered expression host cells should always be accompanied by detailed glycan analysis of the particular therapeutic proteins being produced.ConclusionsOur findings reinforce accumulating evidence that robustly customizing the N-glycosylation pathway in Pichia pastoris to produce particular human-type structures is still an incompletely solved synthetic biology challenge, which will require further innovation to enable safe glycoprotein pharmaceutical production.

Recombinant protein vaccines are safe but elicit low immunological responses. The new generation of adjuvants is currently reversing this situation. Here, a new antigen–adjuvant combination for protection against experimental Chagas disease was assessed. The antigen used in the formulation was a glycosylated mutant inactive trans-sialidase (mTS) that was previously proven to be highly protective against Trypanosoma cruzi infection; here, we show that it can be produced in large quantities and high quality using Pichia pastoris. The adjuvant used in the formulation was ISCOMATRIX (IMX), which was found to be effective and safe in human clinical trials of vaccines designed to control other intracellular infections. Fifteen days after the third immunization, mice immunized with mTS-IMX showed a TS-specific IgG response with titers >106 and high avidity, an increased IgG2a/IgG1 ratio, significant delayed-type hypersensitivity (DTH) reactivity, a balanced production of IFN-γ and IL-10 by splenocytes and a strong IFN-γ secretion by CD8+ T lymphocytes. When these mice where challenged with 1000 trypomastigotes of T. cruzi, all mTS-IMX immunized mice survived, whereas mice immunized with mTS alone, IMX or PBS exhibited high mortality. Remarkably, during acute infection, when the parasitemia is highest in this infection model (day 21), mTS-IMX immunized mice had ∼50 times less parasitemia than non-immunized mice. At this moment and also in the chronic phase, 100 days after infection, tissue presented ∼4.5 times lower parasite load and associated inflammatory infiltrate and lesions. These results indicate that protection against Chagas disease can be achieved by a protein antigen–adjuvant mTS formulation that is compatible with human medicine. Therefore, the current formulation is a highly promising T. cruzi vaccine candidate to be tested in clinical trials. Fil: Bontempi, Iván. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Vicco, Miguel Hernán. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Cabrera, Gabriel Gustavo. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Villar, Silvina Raquel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Rosario. Instituto de Inmunología Clínica y Experimental de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Cs.medicas; Argentina Fil: González, Florencia Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Rosario. Instituto de Inmunología Clínica y Experimental de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Cs.medicas; Argentina Fil: Roggero, Eduardo Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Rosario. Instituto de Inmunología Clínica y Experimental de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Cs.medicas; Argentina Fil: Ameloot, Paul. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; Bélgica Fil: Callewaert, Nico. Vlaams Instituut voor Biotechnologie; Bélgica. University of Ghent; Bélgica Fil: Perez, Ana Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - Rosario. Instituto de Inmunología Clínica y Experimental de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Cs.medicas; Argentina Fil: Marcipar, Ivan Sergio. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

The cysteine-rich secretory/antigen 5/pathogenesis-related 1 (CAP) protein superfamily is composed of a functionally diverse group of members that are found in both eukaryotes and prokaryotes. The excretome/secretome of numerous helminths (parasitic nematodes) contains abundant amounts of CAP members termed activation-associated secreted proteins (ASPs). Although ASPs are necessary for the parasitic life cycle in the host, the current lack of structural and functional information limits both understanding of their actual role in host-parasite interactions and the development of new routes in controlling parasitic infections and diseases. Alleviating this knowledge gap, a 1.85 Å resolution structure of recombinantly produced Oo-ASP-1 from Ostertagia ostertagi, which is one of the most prevalent gastrointestinal parasites in cattle worldwide, was solved. Overall, Oo-ASP-1 displays the common hallmark architecture shared by all CAP-superfamily members, including the N-terminal CAP and C-terminal cysteine-rich domains, but it also reveals a number of highly peculiar features. In agreement with studies of the natively produced protein, the crystal structure shows that Oo-ASP-1 forms a stable dimer that has been found to be primarily maintained via an intermolecular disulfide bridge, hence the small interaction surface of only 306.8 Å(2). Moreover, unlike any other ASP described to date, an additional intramolecular disulfide bridge links the N- and C-termini of each monomer, thereby yielding a quasi-cyclic molecule. Taken together, the insights presented here form an initial step towards a better understanding of the actual biological role(s) that this ASP plays in host-parasite interactions. The structure is also essential to help to define the key regions of the protein suitable for development of ASP-based vaccines, which would enable the current issues surrounding anthelmintic resistance in the treatment of parasitic infections and diseases to be circumvented. journal: Acta Crystallographica Section D: Biological Crystallography content_type: research papers peer_reviewed: Yes review_process: Single blind received: 29 August 2012 accepted: 6 December 2012 published_online: 9 March 2013 supplementary_materials: This article has supplementary materials copyright: © 2013 International Union of Crystallography ispartof: Acta Crystallographica D, Biological Crystallography vol:69 issue:Pt 4 pages:493-503 ispartof: location:United States status: published

UNLABELLED Essentials Thrombin-activatable fibrinolysis inhibitor (TAFI) is a risk factor for cardiovascular disorders. TAFI inhibitory nanobodies represent a promising step in developing profibrinolytic therapeutics. We have solved three crystal structures of TAFI in complex with inhibitory nanobodies. Nanobodies inhibit TAFI through distinct mechanisms and represent novel profibrinolytic leads. SUMMARY Background Thrombin-activatable fibrinolysis inhibitor (TAFI) is converted to activated TAFI (TAFIa) by thrombin, plasmin, or the thrombin-thrombomodulin complex (T/TM). TAFIa is antifibrinolytic, and high levels of TAFIa are associated with an increased risk for cardiovascular disorders. TAFI-inhibitory nanobodies represent a promising approach for developing profibrinolytic therapeutics. Objective To elucidate the molecular mechanisms of inhibition of TAFI activation and TAFIa activity by nanobodies with the use of X-ray crystallography and biochemical characterization. Methods and results We selected two nanobodies for cocrystallization with TAFI. VHH-a204 interferes with all TAFI activation modes, whereas VHH-i83 interferes with T/TM-mediated activation and also inhibits TAFIa activity. The 3.05-A-resolution crystal structure of TAFI-VHH-a204 reveals that the VHH-a204 epitope is localized to the catalytic moiety (CM) in close proximity to the TAFI activation site at Arg92, indicating that VHH-a204 inhibits TAFI activation by steric hindrance. The 2.85-A-resolution crystal structure of TAFI-VHH-i83 reveals that the VHH-i83 epitope is located close to the presumptive thrombomodulin-binding site in the activation peptide (AP). The structure and supporting biochemical assays suggest that VHH-i83 inhibits TAFIa by bridging the AP to the CM following TAFI activation. In addition, the 3.00-A-resolution crystal structure of the triple TAFI-VHH-a204-VHH-i83 complex demonstrates that the two nanobodies can simultaneously bind to TAFI. Conclusions This study provides detailed insights into the molecular mechanisms of TAFI inhibition, and reveals a novel mode of TAFIa inhibition. VHH-a204 and VHH-i83 merit further evaluation as potential profibrinolytic therapeutics.

F18 + Escherichia coli can cause post-weaning diarrhoea and oedema disease in pigs. These diseases are responsible for substantial economic losses, but a vaccine is not available. A good knowledge of the characteristic of the fimbriae is useful for the development of a vaccine composed of the fimbrial virulence factor. F18 fimbriae are composed of the major subunit FedA and the minor subunits FedE and the adhesin FedF. In the present study monoclonal antibodies (mAbs) against FedA and FedF were produced. In addition to their diagnostic value, these mAbs revealed a weaker interaction between FedA and FedF compared to the subunit–subunit interactions in other fimbriae, like type 1 and P pili. Further experiments are needed to investigate if this weak interaction could be one of the reasons for the slow colonisation of the small intestinal mucosa by F18 + E. coli .

Characterization of the interaction between murine tumour necrosis factor and monoclonal antibodies.Ameloot P, Fiers W, Buurman WA, de Baetselier P, Brouckaert P.Department of Molecular Biology, Unit of Molecular Pathophysiology and Experimental Therapy, Flanders Interuniversity Institute for Biotechnology and Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.We characterized the interaction between murine TNF (mTNF) and the neutralizing monoclonal antibodies TN3 and 1F3F3. The epitopes were localized by comparing the detection efficiency for a panel of TNF chimaeric proteins and site-specific muteins in ELISA. Mutation of mTNF amino acid Q131 inhibited the interaction with 1F3F3, whereas mutation of D71/Y72 inhibited the binding to TN3. As D71/Y72 are located in an exposed loop near the TNF intersubunit groove, binding of TN3 promoted the dissociation and/or interfered with the reassociation of subunits into mTNF trimers. 1F3F3, on the other hand, prevented the spontaneous dissociation of bound (hetero)trimeric mTNF.

The bioactivity of tumor necrosis factor (TNF) is mediated by two TNF receptors (TNF-Rs), more particularly TNF-RI and TNF-RII. Although human TNF (hTNF) and murine TNF (mTNF) are very homologous, hTNF binds only to mTNF-RI. By measuring the binding of a panel of mTNF/hTNF chimeras to both mTNF-R, we pinpointed the TNF region that mediates the interaction with mTNF-RII. Using site-specific mutagenesis, we identified amino acids 71-73 and 89 as the main interacting residues. Mutein hTNF-S71D/T72Y/H73 Delta/T89E interacts with both types of mTNF-R and is active in CT6 cell proliferation assays mediated by mTNF-RII. Mutein mTNF-D71S/Y72T/Delta 73H/E89T binds to mTNF-RI only and is no longer active on CT6 cells. However, the L929s cytotoxicity of this mutein (an effect mediated by mTNF-RI triggering) was also 100-fold lower than that of wild-type mTNF due to enhanced dissociation during incubation at subnanomolar concentrations. The additional mutation of amino acid 102, resulting in the mutein mTNF-D71S/Y72T/Delta 73H/E89T/P102Q, restored the trimer stability, which led to an enhanced specific activity on L929s cells. Hence the specific activity of a TNF species is governed not only by its receptor binding characteristics but also by its trimer stability after incubation at subnanomolar concentrations. In conclusion, the mutation of TNF amino acids 71-73, 89, and 102 is sufficient to obtain a mTNF mutein selective for mTNF-RI and a hTNF mutein that, unlike wild-type hTNF, also acts on mTNF-RII.

Tumor necrosis factor (TNF) is a pleiotropic cytokine with a wide range of biological activities including cytotoxicity, immune-cell proliferation, and mediation of inflammatory responses. Mutational analysis of mature TNF has been facilitated by the high expression levels that were obtained in Escherichia coli cells. Furthermore, the fact that mature TNF does not form inclusion bodies, but remains soluble in bacterial extracts, allows a fast and easy characterization. We describe an efficient method for the introduction of a specific mutation in mature murine TNF making use of double-stranded plasmid DNA and two oligonucleotides. Two in vitro protocols are given that allow assessment of the binding of wild-type TNF and/or TNF muteins to TNF receptors (TNFR) (radioligand competition binding and Biacore). The biological activity of wild-type TNF and/or TNF muteins can be assessed in cellular assays. TNF-induced cytotoxicity toward murine L929s cells and human Kym39A6 cells is mediated by interaction with cellular TNFR-I, whereas TNF-induced proliferation of murine CT6 cells is mediated by triggering of cellular TNFR-II.

Tumor necrosis factor (TNF) is a pleiotropic cytokine with a wide range of biological activities including cytotoxicity, immune-cell proliferation, and mediation of inflammatory responses. Mutational analysis of mature TNF has been facilitated by the high expression levels that were obtained in Escherichia coli cells. Furthermore, the fact that mature TNF does not form inclusion bodies, but remains soluble in bacterial extracts, allows a fast and easy characterization. We describe an efficient method for the introduction of a specific mutation in mature murine TNF making use of double-stranded plasmid DNA and two oligonucleotides. Two in vitro protocols are given that allow assessment of the binding of wild-type TNF and/or TNF muteins to TNF receptors (TNFR) (radioligand competition binding and Biacore). The biological activity of wild-type TNF and/or TNF muteins can be assessed in cellular assays. TNF-induced cytotoxicity toward murine L929s cells and human Kym39A6 cells is mediated by interaction with cellular TNFR-I, whereas TNF-induced proliferation of murine CT6 cells is mediated by triggering of cellular TNFR-II.

Item does not contain fulltext In mice, tumor necrosis factor (TNF) displays a selective species specificity. In contrast to murine TNF (mTNF), human TNF (hTNF) only induces lethality at extremely high doses of about 500 microg/mouse, whereas it still has a powerful antitumor activity in combination with interferon-gamma. The observation that hTNF does not interact with the p75 mTNF receptor seemed to provide a plausible explanation for these species-specific biological effects. Experiments in TNF receptor knockout mice and tests with hTNF muteins in baboons did not, however, support this hypothesis. We here show that an mTNF mutein selective for the p55 mTNF receptor induces lethality in a manner comparable to wild-type mTNF, and conclude that other differences between hTNF and mTNF must account for the reduced lethality of hTNF. Pharmacokinetics showed that hTNF is cleared much faster than mTNF or the mTNF mutein used. In contrast to the hardly lethal effect(s) of a bolus administration of hTNF, fractionated repetitive administration of the same total hTNF dose induced lethality. This suggests that prolonged exposure rather than peak levels determine the lethal effects of hTNF in mice. Experiments with receptor and ligand knockouts demonstrated that the difference in pharmacokinetics is independent of an interaction with (soluble) TNF receptor, TNF-induced effects or induction of endogenous TNF. These results show that manipulation of the clearance rate of TNF may broaden the therapeutic range of systemic treatments with TNF.

Sialyltransferases are enzymes responsible for the important sialylation of glycoconjugates. Since crystal structures are not available, other tools are needed to study enzymatic mechanisms. As a model, we used human alpha2,6-sialyltransferase. A putative acceptor-binding domain containing the small and the very small sialyl motifs was randomly mutated. This resulted in enzymes with altered enzymatic activity. Affinity chromatography demonstrated that their binding to donor substrate was maintained. To illustrate the role of the mutated domain in acceptor binding, a method based on surface plasmon resonance was set up. Only at low salt and high acceptor concentration was association of wild-type ST6GalI with asialofetuin demonstrated. As expected, this interaction was affected by cytidine 5'-monophospho-N-acetylneuraminic acid, the donor substrate, which proves the specificity of the interaction. Different types of mutants were found. For some, the drop in activity could be explained by loss in affinity for the acceptor. For others, the catalytic center, but not the acceptor-binding site, was affected. Neither acceptor binding nor catalytic activity were limited to the sialyl motifs. To our knowledge, this is the first example in which surface plasmon resonance is successfully used to demonstrate the binding of a glycosyltransferase to its natural acceptor.

TNF affects many cellular metabolic processes, regulates gene expression, and may induce apoptosis or necrosis dependent on cell type and conditions of exposure. TNF also induces specific alterations in mitochondrial morphology and biochemistry. Ultrastructurally, these alterations include a swollen appearance characterised by increased matrix space and reduced number of cristae [ 13. Biochemical abnormalities include inhibition of electron transport [2], generation of superoxide [ 1,3] and reduction in mitochondrial transmembrane potential [4]. Mitochondria have a central role in the apoptotic and necrotic processes, including in TNF-induced cytotoxicity [5], and TNF-induced functional mitochondrial damage precedes cytotoxicity. It has also recently been reported that TNF induces autophagy in an acute Tlymphoblastic leukemic cell line [6]. Autophagy is a major mechanism of intralysosomal proteolysis occurring in most cell types in both physiological and pathological states [7]. Autophagic vacuoles are formed when portions of the cytoplasm, sometimes including organelles, are surrounded by a sequestering membrane principally derived from the endoplasmic reticulum. These double membrane-bound structures then fuse with lysosomes to form autolysosomes and acquire protein degradative capacity. Autophagy is an energy-requiring process that is responsible for an increase in proteolysis thus enabling an acute cellular response to change in energy availability or expenditure. Autophagy is also a predominant feature of programmed (active) cell death in highly synthetic or secretory cells (type I1 cell death) [8]. Type I1 cell death is morphologically distinct from apoptosis (type I cell death) which classically occurs in highly mitotically active cells and is characterised by predominantly nuclear morphological changes with little autophagy [8]. TNF effects on cells are mediated via two distinct cell-surface receptors of 55/60 kD (TNFR-I) and 75/80 kD (TNFR-II), which are ubiquitously expressed [9]. The receptors utilise both independent and shared intracellular signalling pathways to mediate a variety of effects on cells. Cytotoxic effects are, in the main, mediated by TNFR-I whilst TNFR-I1 has proliferative effects, at least in lymphoid cells. In this study we sought to a) investigate ultrastructural responses to TNF, b) determine which TNF receptor@) mediate these changes, and c) determine if these changes invariably lead to cytotoxicity. Murine 3T3-LI and human preadipocytes (which undergo TNFinduced apoptosis), murine WEHI 164 cells (which undergo TNFinduced necrosis) and human umbilical vein endothelial cells (which are insensitive to TNF) were cultured +/TNF or receptorspecific TNF muteins. Ultrastructural analysis was undertaken by electron microscopy, and apoptosis and necrosis assayed using acridine orange andor annexin V. In all of the cell types studied TNF induced autophagy (Fig 1) in addition to classical mitochondrial morphological changes (Fig 2).

Chimeric plasmids were constructed such that the cloned complete satellite tobacco necrosis virus (STNV) RNA information came under transcriptional control of the leftward promoter (PL) of bacteriophage lambda. The promoter is fully repressed at low temperatures (28 degrees) by the thermolabile repressor product of the lambdacI857 gene, present in the bacterium on a deficient prophage or as part of another plasmid. Synthesis of the STNV coat protein in Escherichia coli could be initiated by heat induction (42 degrees). These in vivo results confirm that the 5'-untranslated region of STNV RNA, preceding the initiating AUG, provides adequate genetic information for efficient translation in the bacterial system. However, fast degradation of the bacterially synthesized STNV coat protein was observed. The use of a protease-deficient strain reduced this breakdown considerably.

Mechanical inoculation of cowpea leaves with cloned full-size copies of satellite tobacco necrosis virus in the presence of tobacco necrosis (helper) virus resulted in the appearance of infectious virus particles. This could be clearly demonstrated by the detection of structural changes in the progeny viral RNA after inoculation with helper virus and hybrid plasmids containing an STNV-DNA copy with small (14-mer) oligodeoxynucleotides inserted at different sites in either the coding or the non-coding region. Furthermore, although orientation and position of the viral cDNA in the different plasmids did not seem to be of major importance for the ensuing infection process, the presence of adjacent complementary homopolymeric regions (dG/dC) at both ends of the STNV nucleotide sequence was necessary. Progeny STNV was obtained which carried oligonucleotide insertions at various positions of the genome.

Background The unfolded protein response (UPR) in eukaryotes upregulates factors that restore ER homeostasis upon protein folding stress and in yeast is activated by a non-conventional splicing of the HAC1 mRNA. The spliced HAC1 mRNA encodes an active transcription factor that binds to UPR-responsive elements in the promoter of UPR target genes. Overexpression of the HAC1 gene of S. cerevisiae can reportedly lead to increased production of heterologous proteins. To further such studies in the biotechnology favored yeast Pichia pastoris, we cloned and characterized the P. pastoris HAC1 gene and the splice event. Results We identified the HAC1 homologue of P. pastoris and its splice sites. Surprisingly, we could not find evidence for the non-spliced HAC1 mRNA when P. pastoris was cultivated in a standard growth medium without any endoplasmic reticulum stress inducers, indicating that the UPR is constitutively active to some extent in this organism. After identification of the sequence encoding active Hac1p we evaluated the effect of its overexpression in Pichia. The KAR2 UPR-responsive gene was strongly upregulated. Electron microscopy revealed an expansion of the intracellular membranes in Hac1p-overexpressing strains. We then evaluated the effect of inducible and constitutive UPR induction on the production of secreted, surface displayed and membrane proteins. Wherever Hac1p overexpression affected heterologous protein expression levels, this effect was always stronger when Hac1p expression was inducible rather than constitutive. Depending on the heterologous protein, co-expression of Hac1p increased, decreased or had no effect on expression level. Moreover, α-mating factor prepro signal processing of a G-protein coupled receptor was more efficient with Hac1p overexpression; resulting in a significantly improved homogeneity. Conclusions Overexpression of P. pastoris Hac1p can be used to increase the production of heterologous proteins but needs to be evaluated on a case by case basis. Inducible Hac1p expression is more effective than constitutive expression. Correct processing and thus homogeneity of proteins that are difficult to express, such as GPCRs, can be increased by co-expression with Hac1p.