Prion protein-related proteins from zebrafish are complex glycosylated and contain a glycosylphosphatidylinositol anchor

A hallmark of prion diseases in mammals is a conformational transition of the cellular prion protein (PrP(C)) into a pathogenic isoform termed PrP(Sc). PrP(C) is highly conserved in mammals, moreover, genes of PrP-related proteins have been recently identified in fish. While there is only little sequence homology to mammalian PrP, PrP-related fish proteins were predicted to be modified with N-linked glycans and a C-terminal glycosylphosphatidylinositol (GPI) anchor. We biochemically characterized two PrP-related proteins from zebrafish in cultured cells and show that both zePrP1 and zeSho2 are imported into the endoplasmic reticulum and are post-translationally modified with complex glycans and a C-terminal GPI anchor.     

Generation of Peptide mimics of the epitope recognized by trastuzumab on the oncogenic protein Her-2/neu

Immunizations with the oncogenic protein Her-2/neu elicit Abs exerting diverse biological effects--depending on epitope specificity, tumor growth may be inhibited or enhanced. Trastuzumab (herceptin) is a growth-inhibitory humanized monoclonal anti-Her-2/neu Ab, currently used for passive immunotherapy in the treatment of breast cancer. However, Ab therapies are expensive and have to be repeatedly administered for long periods of time. In contrast, active immunizations produce ongoing immune responses. Therefore, the study aims to generate peptide mimics of the epitope recognized by trastuzumab for vaccine formulation, ensuring the subsequent induction of tumor growth inhibitory Abs. We used the phage display technique to generate epitope mimics, mimotopes, complementing the screening Ab trastuzumab. Five candidate mimotopes were isolated from a constrained 10 mer library. These peptides were specifically recognized by trastuzumab, and showed distinctive mimicry with Her-2/neu in two experimental setups. Subsequently, immunogenicity of a selected mimotope was examined in BALB/c mice. Immunizations with a synthetic mimotope conjugated to tetanus toxoid resulted in Abs recognizing Her-2/neu in a blotted cell lysate as well as on the SK-BR-3 cell surface. Analogous to trastuzumab, the induced Abs caused internalization of the receptor from the cell surface to endosomal vesicles. These results indicate that the selected mimotopes are suitable for formulation of a breast cancer vaccine because the resulting Abs show similar biological features as trastuzumab.     

Double staining of intracellular cytokine proteins and T-lymphocyte subsets. Evaluation of the method in blood and bronchoalveolar lavage fluid

An immunocytochemical staining method has been developed for simultaneous staining of both cell surface markers (CD4 and CD8) and intracellular cytokine proteins IFN-, IL-4 and IL-5. Cell surface molecules were visualized with alkaline phosphatase, which was developed by Fast Blue BB. Intracellular cytokine proteins were detected by amino-ethyl carbazole. We applied this technique to T cells from T-cell lines and T-cell clones, peripheral blood mononuclear cells and broncho-alveolar lavage fluid cells. Cells were used either unstimulated or stimulated for 4h with 1ng/ml PMA and 1g/ml ionomycin, which proved to be an optimal stimulus taking cytokine staining, cell recovery and cell viability into account. We studied peripheral blood mononuclear cells from healthy subjects and found that without in vitro stimulation on average 0.4% of the cells were IFN- positive cells. In unstimulated broncho-alveolar lavage fluid cells of the 2 allergic asthmatic subjects studied so far we found higher numbers of cytokine-positive cells (up to 22% of the lymphocytes being IL-4⁺ cells). By in vitro stimulation, the numbers of cytokine-positive peripheral blood mononuclear cells from the healthy subjects were increased to maximally 5% IFN-⁺ cells. In stimulated lavage fluid cells from allergic asthmatic subjects maximally 34% of the lymphocytes became IFN-⁺. We conclude that this method allows detection of intracellular cytokine proteins in both CD4⁺ and CD8⁺ T cells without the need for stimulating the cells in vitro. In vitro stimulation may change the cytokine profile detected.     

A Targeted LC‐MS Strategy for Low‐Abundant HLA Class‐I‐Presented Peptide Detection Identifies Novel Human Papillomavirus T‐Cell Epitopes

For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation‐derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC‐MS³‐based targeted detection of low‐abundant human leukocyte antigen (HLA) class‐I‐presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen‐derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA‐peptide complexes, while keeping high isolation yields of low‐abundant target peptides. The subsequent targeted LC‐MS³ detection allowed for increased sensitivity, which resulted in successful detection of the known HLA‐A2‐restricted epitope E7_11–19 and ten additional E7‐derived peptides on the surface of HPV16‐transformed cells. T‐cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low‐abundant candidate epitopes to be true immunotherapy targets.     

Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications

MOTIVATION: The analysis of metabolic processes is becoming increasingly important to our understanding of complex biological systems and disease states. Nuclear magnetic resonance spectroscopy (NMR) is a particularly relevant technology in this respect, since the NMR signals provide a quantitative measure of the metabolite concentrations. However, due to the complexity of the spectra typical of biological samples, the demands of clinical and high-throughput analysis will only be fully met by a system capable of reliable, automatic processing of the spectra. An initial step in this direction has been taken by Targeted Profiling (TP), employing a set of known and predicted metabolite signatures fitted against the signal. However, an accurate fitting procedure for (1)H NMR data is complicated by shift uncertainties in the peak systems caused by measurement imperfections. These uncertainties have a large impact on the accuracy of identification and quantification and currently require compensation by very time consuming manual interactions. Here, we present an approach, termed Extended Targeted Profiling (ETP), that estimates shift uncertainties based on a genetic algorithm (GA) combined with a least squares optimization (LSQO). The estimated shifts are used to correct the known metabolite signatures leading to significantly improved identification and quantification. In this way, use of the automated system significantly reduces the effort normally associated with manual processing and paves the way for reliable, high-throughput analysis of complex NMR spectra. RESULTS: The results indicate that using simultaneous shift uncertainty correction and least squares fitting significantly improves the identification and quantification results for (1)H NMR data in comparison to the standard targeted profiling approach and compares favorably with the results obtained by manual expert analysis. Preservation of the functional structure of the NMR spectra makes this approach more realistic than simple binning strategies.     

Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon sulfolobus solfataricus

We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2-4 (optimum 3.5) and a temperature of 75-80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.     

Divergent Molecular Evolution of the Mitochondrial Sulfhydryl:Cytochrome c Oxidoreductase Erv in Opisthokonts and Parasitic Protists

Mia40 and the sulfhydryl:cytochrome c oxidoreductase Erv1/ALR are essential for oxidative protein import into the mitochondrial intermembrane space in yeast and mammals. Although mitochondrial protein import is functionally conserved in the course of evolution, many organisms seem to lack Mia40. Moreover, except for in organello import studies and in silico analyses, nothing is known about the function and properties of protist Erv homologues. Here we compared Erv homologues from yeast, the kinetoplastid parasite Leishmania tarentolae, and the non-related malaria parasite Plasmodium falciparum. Both parasite proteins have altered cysteine motifs, formed intermolecular disulfide bonds in vitro and in vivo, and could not replace Erv1 from yeast despite successful mitochondrial protein import in vivo. To analyze its enzymatic activity, we established the expression and purification of recombinant full-length L. tarentolae Erv and compared the mechanism with related and non-related flavoproteins. Enzyme assays indeed confirmed an electron transferase activity with equine and yeast cytochrome c, suggesting a conservation of the enzymatic activity in different eukaryotic lineages. However, although Erv and non-related flavoproteins are intriguing examples of convergent molecular evolution resulting in similar enzyme properties, the mechanisms of Erv homologues from parasitic protists and opisthokonts differ significantly. In summary, the Erv-mediated reduction of cytochrome c might be highly conserved throughout evolution despite the apparent absence of Mia40 in many eukaryotes. Nevertheless, the knowledge on mitochondrial protein import in yeast and mammals cannot be generally transferred to all other eukaryotes, and the corresponding pathways, components, and mechanisms remain to be analyzed.