CST-II’s recognition domain for acceptor substrates in α-(2→8)-sialylations

CST-II is a bacterial sialyltransferase known for its ability to perform α-(2→8)-sialylations using GM₃ related trisaccharide substrates. Previously, we probed the enzyme’s substrate specificity and developed an efficient synthesis for α-(2→8)-oligosialosides, and we suggested that CST-II could have a very small substrate recognition domain. Here we report our full studies on CST-II’s recognition feature for acceptor substrates. The current study further demonstrates the versatility of CST-II in preparing complex oligosaccharides that contain α-(2→8)-oligosialyl moieties.     

Genotype-phenotype correlations in Lesch-Nyhan disease: moving beyond the gene

Lesch-Nyhan disease and its attenuated variants are caused by mutations in the HPRT1 gene, which encodes the purine recycling enzyme hypoxanthine-guanine phosphoribosyltransferase. The mutations are heterogeneous, with more than 400 different mutations already documented. Prior efforts to correlate variations in the clinical phenotype with different mutations have suggested that milder phenotypes typically are associated with mutants that permit some residual enzyme function, whereas the most severe phenotype is associated with null mutants. However, multiple exceptions to this concept have been reported. In the current studies 44 HPRT1 mutations associated with a wide spectrum of clinical phenotypes were reconstructed by site-directed mutagenesis, the mutant enzymes were expressed in vitro and purified, and their kinetic properties were examined toward their substrates hypoxanthine, guanine, and phosphoribosylpyrophosphate. The results provide strong evidence for a correlation between disease severity and residual catalytic activity of the enzyme (k(cat)) toward each of its substrates as well as several mechanisms that result in exceptions to this correlation. There was no correlation between disease severity and the affinity of the enzyme for its substrates (K(m)). These studies provide a valuable model for understanding general principles of genotype-phenotype correlations in human disease, as the mechanisms involved are applicable to many other disorders.     

Supercritical carbon dioxide pretreatment of corn stover and switchgrass for lignocellulosic ethanol production

Supercritical CO₂ (SC-CO₂), a green solvent suitable for a mobile lignocellulosic biomass processor, was used to pretreat corn stover and switchgrass at various temperatures and pressures. The CO₂ pressure was released as quickly as possible by opening a quick release valve during the pretreatment. The biomass was hydrolyzed after pretreatment using cellulase combined with β-glucosidase. The hydrolysate was analyzed for the amount of glucose released. Glucose yields from corn stover samples pretreated with SC-CO₂ were higher than the untreated sample’s 12% glucose yield (12 g/100 g dry biomass) and the highest glucose yield of 30% was achieved with SC-CO₂ pretreatment at 3500 psi and 150 °C for 60 min. The pretreatment method showed very limited improvement (14% vs. 12%) in glucose yield for switchgrass. X-ray diffraction results indicated no change in crystallinity of the SC-CO₂ treated corn stover when compared to the untreated, while SEM images showed an increase in surface area.     

Successive soil treatment with captan or oxytetracycline affects non-target microorganisms

Changes in microbial biomass and activity were determined in a sandy-loam soil treated with successive dosages of oxytetracycline (a bactericide) or captan (a fungicide) throughout 98 days of incubation under laboratory conditions. The numbers of culturable bacteria and fungi, total bacterial and fungal biomass (as amounts of phospholipid fatty acids, PLFA), the fungal/bacterial ratio, activities of acid and alkaline phosphatases and urease as well as concentrations of N-NH₄ ⁺ and N-NO₃ ⁻ were assessed. Both oxytetracycline and captan significantly decreased numbers of culturable bacteria whereas total bacterial biomass (bactPLFA) was not affected. Oxytetracycline did not effect on the fungal biomass, however their numbers were reduced after the first and second time of soil amendment with the bactericide. Conversely, fungal numbers and biomass (PLFA 18:2ω6,9) significantly decreased in response to soil treatment with the fungicide. Compared to oxytetracycline, captan significantly decreased activities of acid and alkaline phosphatases. For urease activity, the decreased activity was only observed in the soil after the third dosage of captan. Both biocides significantly increased concentrations of N-NH₄ ⁺ and decreased concentrations of N-NO₃ ⁻ after the soil treatments. The results of this study indicate that successive soil treatment with oxytetracycline or captan dosages may negatively affect non-target soil microorganisms and their activities.     

Surprisingly high correlation between early and late stages in non-two-state protein folding

We collected quantitative kinetic data on early and late stages of folding in non-two-state proteins from the literature, and studied the relationship between the kinetics of the two stages. There was a surprisingly high correlation between the rate constants of these stages. The correlation coefficient of the logarithmic rate constants was as high as 0.97, which could not be caused by chance. We also studied relationships of the logarithmic rate constants of the two stages with native three-dimensional structures represented by the residue-residue contact map. There were again surprisingly high correlations between the logarithmic rate constants and the number of non-local contact clusters obtained from the contact maps. Because the number of non-local contact clusters represents overall arrangement of substructures in a native protein, the results strongly suggested the importance of the arrangement of the substructures for the kinetics of both early and late stages of protein folding.     

RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo

RtcB enzymes are novel RNA ligases that join 2',3'-cyclic phosphate and 5'-OH ends. The phylogenetic distribution of RtcB points to its candidacy as a tRNA splicing/repair enzyme. Here we show that Escherichia coli RtcB is competent and sufficient for tRNA splicing in vivo by virtue of its ability to complement growth of yeast cells that lack the endogenous "healing/sealing-type" tRNA ligase Trl1. RtcB also protects yeast trl1Δ cells against a fungal ribotoxin that incises the anticodon loop of cellular tRNAs. Moreover, RtcB can replace Trl1 as the catalyst of HAC1 mRNA splicing during the unfolded protein response. Thus, RtcB is a bona fide RNA repair enzyme with broad physiological actions. Biochemical analysis of RtcB highlights the uniqueness of its active site and catalytic mechanism. Our findings draw attention to tRNA ligase as a promising drug target.     

Amyloid beta proteins inhibit Cl(-)-ATPase activity in cultured rat hippocampal neurons

Cl(-)-ATPase in the CNS is a candidate for an outwardly directed neuronal Cl(-) transporter requiring phosphatidylinositol-4-phosphate (PI4P) for its optimal activity. To test its pathophysiological changes in a phosphatidylinositol (PI) metabolism disorder, the effects of neurotoxic factors in Alzheimer's disease (AD), amyloid beta proteins (Abetas), on the Cl(-)-ATPase activity were examined using primary cultured rat hippocampal neurons. Amyloid beta proteins (1-40, 1-42 and 25-35) concentration-dependently (1-100 nM) and time-dependently (from 1 h to 6 day) decreased Cl(-)-ATPase activity and elevated intracellular Cl(-) concentrations ([Cl(-)]i), Abeta25-35 being the most potent. Addition of inositol or 8-Br-cyclic GMP completely reversed these Abeta-induced changes. The recoveries in enzyme activity were attenuated by an inhibitor of PI 4-kinase, 10 microM wortmannin or 20 microM quercetin, but not by a PI 3-kinase inhibitor, 50 nM wortmannin or 10 microM LY294002. The PI, PIP and PIP2 levels of the plasma membrane-rich fraction were lower in the Abeta-treated cells as compared with each control. In the Abeta-exposed culture, but not in control, stimulation by 10 microM glutamate for 10 min significantly increased fragmentation of DNA and decreased cell viability. Addition of inositol or 8-Br-cyclic GMP prevented the effect of Abeta-treatment on the neurotoxicity of glutamate. Thus, Abetas reduce neuronal Cl(-)-ATPase activity, resulting in an increase in [Cl(-)]i probably by lowering PI4P levels, and this may reflect a pre-apoptotic condition in early pathophysiological profiles of AD.     

An end to insight? New Caledonian crows can spontaneously solve problems without planning their actions

Animals rarely solve problems spontaneously. Some bird species, however, can immediately find a solution to the string-pulling problem. They are able to rapidly gain access to food hung on the end of a long string by repeatedly pulling and then stepping on the string. It is currently unclear whether these spontaneous solutions are produced by insight or by a perceptual-motor feedback loop. Here, we presented New Caledonian crows and humans with a novel horizontal string-pulling task. While the humans succeeded, no individual crow showed a significant preference for the connected string, and all but one failed to gain the food even once. These results clearly show that string pulling in New Caledonian crows is generated not by insight, but by perceptual feedback. Animals can spontaneously solve problems without planning their actions.