An optimized method for extraction and quantification of nucleotides and nucleotide sugars from mammalian cells

Glycosylation is a critical attribute of therapeutic proteins given its impact on the clinical safety and efficacy of these molecules. The biochemical process of glycosylation is inextricably dependent on metabolism and ensuing availability of nucleotides and nucleotide sugars (NSs) during cell culture. Herein, we present a comprehensive methodology to extract and quantify these metabolites from cultured cells. To establish the full protocol, two methods for the extraction of these compounds were evaluated for efficiency, and the requirement for quenching and washing the sample was assessed. A chromatographic method based on anion exchange has been optimized to separate and quantify eight nucleotides and nine NSs in less than 30 min. Degradation of nucleotides and NSs under extraction conditions was evaluated to aid in selection of the most efficient extraction protocol. We conclude that the optimized chromatographic method is quick, robust, and sensitive for quantifying nucleotides and NSs. Furthermore, our results show that samples taken from cell culture should be treated with 50% v/v acetonitrile and do not require quenching or washing for reliable extraction of nucleotides and NSs. This comprehensive protocol should prove useful in determining the impact of nucleotide and NS metabolism on protein glycosylation.     

Long-term selenium supplementation of humans: Selenium status and relationships between selenium concentrations in skeletal muscle and indicator materials

Supplementation with elevated doses of l-selenomethionine (SeM) or selenium-enriched yeast that contains SeM as the main selenium species is frequently used as a protective or therapeutic measure. Information on the effects of long-term selenium supplementation on the body selenium status is, however, rather scarce. We therefore investigated fifteen male test persons who had taken selenium yeast and/or SeM supplements in medium doses of 62.5–125 μg Se/day or high doses of 200–262.5 μg Se/day for periods ranging from 1 year to 24 years. Seven non-supplemented men served as controls. As skeletal muscle is the main selenium pool, thigh muscle biopsy samples were taken. The selenium concentrations in these biopsies and in samples of the indicator materials blood, blood plasma, blood cells, head hair and toenails were determined by neutron activation analysis. Compared with the controls, the muscle selenium level was raised with additional selenium supplementation, but the relative increase in the mean muscle selenium concentration (by factors of about 1.6 and 2 for the medium and high doses, respectively) was lower than that in the selenium intake. Highly significant correlations found between the selenium concentrations in muscle and whole blood (R=0.90), red blood cells (R=0.91), blood plasma (R=0.87), head hair (R=0.89) and toenails (R=0.85) show that in humans supplemented in this way the selenium status can be assessed in a relatively easy way by analysis of the selenium retention in these indicator materials.     

Carbohydrate esterases of family 2 are 6-O-deacetylases

Three acetyl esterases (AcEs) from the saprophytic bacteria Cellvibrio japonicus and Clostridium thermocellum, members of the carbohydrate esterase (CE) family 2, were tested for their activity against a series of model substrates including partially acetylated gluco-, manno- and xylopyranosides. All three enzymes showed a strong preference for deacetylation of the 6-position in aldohexoses. This regioselectivity is different from that of typical acetylxylan esterases (AcXEs). In aqueous medium saturated with vinyl acetate, the CE-2 enzymes catalyzed transacetylation to the same position, i.e., to the primary hydroxyl group of mono- and disaccharides. Xylose and xylooligosaccharides did not serve as acetyl group acceptors, therefore the CE-2 enzymes appear to be 6-O-deacetylases.     

Expression of the Prion Protein Family Member Shadoo Causes Drug Hypersensitivity That Is Diminished by the Coexpression of the Wild Type Prion Protein

The prion protein (PrP) seems to exert both neuroprotective and neurotoxic activities. The toxic activities are associated with the C-terminal globular parts in the absence of the flexible N terminus, specifically the hydrophobic domain (HD) or the central region (CR). The wild type prion protein (PrP-WT), having an intact flexible part, exhibits neuroprotective qualities by virtue of diminishing many of the cytotoxic effects of these mutant prion proteins (PrPΔHD and PrPΔCR) when coexpressed. The prion protein family member Doppel, which possesses a three-dimensional fold similar to the C-terminal part of PrP, is also harmful to neuronal and other cells in various models, a phenotype that can also be eliminated by the coexpression of PrP-WT. In contrast, another prion protein family member, Shadoo (Sho), a natively disordered protein possessing structural features similar to the flexible N-terminal tail of PrP, exhibits PrP-WT-like protective properties. Here, we report that, contrary to expectations, Sho expression in SH-SY5Y or HEK293 cells induces the same toxic phenotype of drug hypersensitivity as PrPΔCR. This effect is exhibited in a dose-dependent manner and is also counteracted by the coexpression of PrP-WT. The opposing effects of Shadoo in different model systems revealed here may be explored to help discern the relationship of the various toxic activities of mutant PrPs with each other and the neurotoxic effects seen in neurodegenerative diseases, such as transmissible spongiform encephalopathy and Alzheimer disease.     

The brain selenoproteome: priorities in the hierarchy and different levels of selenium homeostasis in the brain of selenium-deficient rats

The application of radionuclides for the localization of essential trace elements in vivo and the characterization of their binding proteins is a story of intermittently made improvements of the techniques used for their detection. In this study we present the use of neutron activation analysis and different autoradiographic imaging methods including real-time digital autoradiography to reveal new insights in the hierarchy of selenium homeostasis. Selenoproteins containing the essential trace element selenium play important roles in the CNS. Although the CNS does not show the highest selenium concentration in the case of selenium-sufficient supply in comparison with other organs, it shows a high priority for selenium uptake and retention in the case of dietary selenium deficiency. To characterize the hierarchy of selenium supply in the brain, in vivo radiotracer labeling with ⁷⁵Se in rats with different selenium status was combined with autoradiographic detection of ⁷⁵Se in brain tissue sections and ⁷⁵Se-labeled selenoproteins after protein separation by two-dimensional gel electrophoresis. This study demonstrates significant differences in the uptake of ⁷⁵Se into the brain of rats with different selenium status. A brain region-specific uptake pattern of the radiotracer ⁷⁵Se in selenium-deficient rats could be revealed and the CSF was identified as a key part of the brain selenium homeostasis.     

Identification of type I iodothyronine 5'-deiodinase as a selenoenzyme

A 27.8 kDa membrane selenoprotein was previously identified in rat thyroid, liver and kidney, the tissues with the highest activities of type I iodothyronine 5'-deiodinase. This membrane enzyme catalyzes the deiodination of L-thyroxine to the biologically active thyroid hormone 3,3',5-triiodothyronine. A decrease in the activity of this enzyme, observed here in the liver of selenium-deficient rats, was found to be due to the absence of a selenium-dependent membrane-bound component. By chemical and enzymatic fragmentation of the 75Se-labeled selenoprotein and of the 27 kDa substrate binding type I 5'-deiodinase subunit, affinity-labeled with N-bromoacetyl-[125I]L-thyroxine, and comparison of the tracer distribution in the peptide fragments the identity of the two proteins was shown. The data indicate that the deiodinase subunit contains one selenium atom per molecule and suggest that a highly reactive selenocysteine is the residue essential for the catalysis of 5'-deiodination. From the results it can be concluded that type I iodothyronine 5'-deiodinase is a selenoenzyme.     

Specific DNA binding by the homeodomain Nkx2.5(C56S): detection of impaired DNA or unfolded protein by isothermal titration calorimetry

Titrations of specific 18-bp duplex DNA with the cardiac-specific homeodomain Nkx2.5(C56S) have utilized an ultrasensitive isothermal titration calorimeter (ITC). As the free DNA nears depletion, we observe large apparent decreases in the binding enthalpy when the DNA is impaired or when the temperature is sufficiently high to produce some unfolding of the free protein. Either effect can be attributed to refolding of the biopolymer that occurs as a result of stabilization due to the large favorable change in free energy on the homeodomain binding to DNA (-49.4 kJ/mol at 298 K). In either case, thermodynamic parameters obtained in such ITC experiments are unreliable. By using a lower temperature (85 vs. 95 degrees C) during the annealing of complementary DNA strands, damage of the 18-bp duplex DNA (T(m) = 72 degrees C) is avoided, and titrations with the homeodomain are normal at temperatures from 10 to 40 degrees C when >95% of the protein is folded. Under the latter conditions, the heat capacity plot is linear with a DeltaC(p) value of -0.80 +/- 0.03 kJ K(-1) mol(-1), which is more negative than that calculated from the burial of solvent accessible surface areas (-0.64 +/- 0.05 kJ K(-1) mol(-1)), consistent with water structures being at the protein-DNA interfaces.     

CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability

Metabolic modeling has emerged as a key tool for the characterization of biopharmaceutical cell culture processes. Metabolic models have also been instrumental in identifying genetic engineering targets and developing feeding strategies that optimize the growth and productivity of Chinese hamster ovary (CHO) cells. Despite their success, metabolic models of CHO cells still present considerable challenges. Genome-scale metabolic models (GeMs) of CHO cells are very large (>6000 reactions) and are difficult to constrain to yield physiologically consistent flux distributions. The large scale of GeMs also makes the interpretation of their outputs difficult. To address these challenges, we have developed CHOmpact, a reduced metabolic network that encompasses 101 metabolites linked through 144 reactions. Our compact reaction network allows us to deploy robust, nonlinear optimization and ensure that the computed flux distributions are physiologically consistent. Furthermore, our CHOmpact model delivers enhanced interpretability of simulation results and has allowed us to identify the mechanisms governing shifts in the anaplerotic consumption of asparagine and glutamate as well as an important mechanism of ammonia detoxification within mitochondria. CHOmpact, thus, addresses key challenges of large-scale metabolic models and will serve as a platform to develop dynamic metabolic models for the control and optimization of biopharmaceutical cell culture processes.