Activity of hyperthermophilic glycosynthases is significantly enhanced at acidic pH

We have previously shown that the hyperthermophilic glycosynthase from Sulfolobus solfataricus (Ssbeta-glyE387G) can promote the synthesis of branched oligosaccharides from activated beta-glycosides, at pH 6.5, in the presence of 2 M sodium formate as an external nucleophile. In an effort to increase the synthetic potential of hyperthermophilic glycosynthases, we report a new method to reactivate the Ssbeta-glyE387G glycosynthase and two novel mutants in the nucleophile of the beta-glycosidases from the hyperthermophilic Archaea Thermosphaera aggregans (Tabeta-gly) and Pyrococcus furiosus (CelB). We describe here that, at pH 3.0 and low concentrations of sodium formate buffer, the three hyperthermophilic glycosynthases show k(cat) values similar to those of the wild-type enzymes and 17-fold higher than those observed at the usual reactivation conditions in 2 M sodium formate at pH 6.5. Moreover, at acidic pH the three reactivated mutants have wide substrate specificity and improved efficiency in the synthetic reaction. The data reported suggest that the reactivation conditions modify the ionization state of the residue acting as an acid/base catalyst. This new reactivation method can be of general applicability on hyperthermophilic glycosynthases whose intrinsic stability allows their exploitation as synthetic tools at low pH.     

Genome-specific higher-order background models to improve motif detection

Motif detection based on Gibbs sampling is a common procedure used to retrieve regulatory motifs in silico. Using a species-specific background model was previously shown to increase the robustness of the algorithm. Here, we demonstrate that selecting a non-species-adapted background model can have an adverse effect on the results of motif detection. The large differences in the average nucleotide composition of prokaryotic sequences exacerbate the problem of exchanging background models. Therefore, we have developed complex background models for all prokaryotic species with available genome sequences.     

Selective interactions between vertebrate polycomb homologs and the SUV39H1 histone lysine methyltransferase suggest that histone H3-K9 methylation contributes to chromosomal targeting of Polycomb group proteins

Polycomb group (PcG) proteins form multimeric chromatin-associated protein complexes that are involved in heritable repression of gene activity. Two distinct human PcG complexes have been characterized. The EED/EZH2 PcG complex utilizes histone deacetylation to repress gene activity. The HPC/HPH PcG complex contains the HPH, RING1, BMI1, and HPC proteins. Here we show that vertebrate Polycomb homologs HPC2 and XPc2, but not M33/MPc1, interact with the histone lysine methyltransferase (HMTase) SUV39H1 both in vitro and in vivo. We further find that overexpression of SUV39H1 induces selective nuclear relocalization of HPC/HPH PcG proteins but not of the EED/EZH2 PcG proteins. This SUV39H1-dependent relocalization concentrates the HPC/HPH PcG proteins to the large pericentromeric heterochromatin domains (1q12) on human chromosome 1. Within these PcG domains we observe increased H3-K9 methylation. Finally, we show that H3-K9 HMTase activity is associated with endogenous HPC2. Our findings suggest a role for the SUV39H1 HMTase and histone H3-K9 methylation in the targeting of human HPC/HPH PcG proteins to modified chromatin structures.     

Reduction of blood pressure,plasma cholesterol,and atherosclerosis by elevated endothelial nitric oxide

In the vascular system, nitric oxide is generated by endothelial NO synthase (eNOS). NO has pleiotropic effects, most of which are believed to be atheroprotective. Therefore, it has been argued that patients suffering from cardiovascular disease could benefit from an increase in eNOS activity. However, increased NO production can cause oxidative damage, cell toxicity, and apoptosis and hence could be atherogenic rather than beneficial. To study the in vivo effects of increased eNOS activity, we created transgenic mice overexpressing human eNOS. Aortic blood pressure was approximately 20 mm Hg lower in the transgenic mice compared with control mice because of lower systemic vascular resistance. The effects of eNOS overexpression on diet-induced atherosclerosis were studied in apolipoprotein E-deficient mice. Elevation of eNOS activity decreased blood pressure ( approximately 20 mm Hg) and plasma levels of cholesterol ( approximately 17%), resulting in a reduction in atherosclerotic lesions by 40%. We conclude that an increase in eNOS activity is beneficial and provides protection against atherosclerosis.     

Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues

A beta-mannosidase gene (PH0501) was identified in the Pyrococcus horikoshii genome and cloned and expressed in E. coli. The purified enzyme (BglB) was most specific for the hydrolysis of p-nitrophenyl-beta-D-mannopyranoside (pNP-Man) (Km: 0.44 mM) with a low turnover rate (kcat: 4.3 s(-1)). The beta-mannosidase has been classified as a member of family 1 of glycoside hydrolases. Sequence alignments and homology modeling showed an apparent conservation of its active site region with, remarkably, two unique active site residues, Gln77 and Asp206. These residues are an arginine and asparagine residue in all other known family 1 enzymes, which interact with the catalytic nucleophile and equatorial C2-hydroxyl group of substrates, respectively. The unique residues of P. horikoshii BglB were introduced in the highly active beta-glucosidase CelB of Pyrococcus furiosus and vice versa, yielding two single and one double mutant for each enzyme. In CelB, both substitutions R77Q and N206D increased the specificity for mannosides and reduced hydrolysis rates 10-fold. In contrast, BglB D206N showed 10-fold increased hydrolysis rates and 35-fold increased affinity for the hydrolysis of glucosides. In combination with inhibitor studies, it was concluded that the substituted residues participate in the ground-state binding of substrates with an equatorial C2-hydroxyl group, but contribute most to transition-state stabilization. The unique activity profile of BglB seems to be caused by an altered interaction between the enzyme and C2-hydroxyl of the substrate and a specifically increased affinity for mannose that results from Asp206.     

Persistence of tertiary structure in 7.9 M guanidinium chloride: the case of endo-beta-1,3-glucanase from Pyrococcus furiosus

The Pyrococcus furiosus endo-beta-1,3-glucanase belongs to the subfamily of laminarinase, which can be classified as "all beta proteins" as confirmed by deconvolution of far-UV CD and FTIR spectra. The persistence of a significant amount of tertiary structure in 7.9 M GdmCl, as indicated by near-UV CD spectroscopy, accompanied by a red-shift of the maximum fluorescence emission wavelength is a peculiar property of this hyperthermophilic endoglucanase. The possibility to observe tertiary structure elements under extremely denaturing conditions is notable and is limited to only a few examples. The unusual resistance toward guanidinium chloride denaturation is paralleled by a notable stability at extremely low pH and at high temperature. The analysis of the protein spectral properties indicates that the secondary structure elements are preserved down to pH 1.0 and up to 90 degrees C at pH 7.4 and pH 3.0. The study of the conditions that determine the persistence of residual structure at high denaturant concentration and the examination of these structures are particularly interesting because these state(s) may be preliminary or coincident with the coalescence of protein aggregates or to the formation of amyloid-like fibrils, and they may serve as seeds of protein folding.     

INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling

INCLUSive allows automatic multistep analysis of microarray data (clustering and motif finding). The clustering algorithm (adaptive quality-based clustering) groups together genes with highly similar expression profiles. The upstream sequences of the genes belonging to a cluster are automatically retrieved from GenBank and can be fed directly into Motif Sampler, a Gibbs sampling algorithm that retrieves statistically over-represented motifs in sets of sequences, in this case upstream regions of co-expressed genes.     

Importance of the gradient in photosynthetically active radiation in a vegetation stand for leaf nitrogen allocation in two monocotyledons

Carex acutiformis and Brachypodium pinnatum were grown with a uniform distribution of photosynthetic photon flux density (PFD) with height, and in a vertical PFD gradient similar to the PFD gradient in a leaf canopy. Distribution of organic leaf N and light-saturated rates of photosynthesis were determined. These parameters were also determined on plants growing in a natural vegetation stand. The effect of a PFD gradient was compared with the effect of a leaf canopy. In Brachypodium, plants growing in a vegetation stand had increasing leaf N with plant height. However, distribution of leaf N was not influenced by the PFD gradient treatment. The gradient of leaf N in plants growing in a leaf canopy was not due to differences within the long, mostly erect, leaves but to differences between leaves. In Carex, however, the PFD gradient caused a clear increase of leaf N with height in individual leaves and thus also in plants. The leaf N gradient was similar to that of plants growing in a leaf canopy. Leaf N distribution was not affected by nutrient availability in Carex. In most cases, photosynthesis was positively related to leaf N. Hence, lightsaturated rates of photosynthesis increased towards the top of the plants growing in leaf canopies in both species and, in Carex, also in the PFD gradient, thus contributing to increased N use efficiency for photosynthesis of the whole plant. It is concluded that in Carex the PFD gradient is the main environmental signal for leaf N allocation in response to shading in a leaf canopy, but one or more other signals must be involved in Brachypodium.     

Application of Stable Isotope Tracers to Studies of Zooplankton Feeding,using the Rotifer <Emphasis Type="Italic">Brachionus calyciflorus</Emphasis> as an Example

We present a protocol and calculation methods for the determination of zooplankton ingestion and assimilation rates with stable isotope tracers. These methods have been developed from experiments with the rotifer Brachionus calyciflorus that had been fed ¹³C-labelled Scenedesmus obliquus. Stable isotope tracers offer the same advantages as radioisotopes. These include the possibility for direct and accurate quantification of ingestion and assimilation rates, short sample analysis times and low animal densities requirements. However, the use of stable isotope tracers requires relatively long sample preparation times and specialist equipment and is, thus, relatively costly for most laboratories. The application of stable isotope tracers in zooplankton feeding studies offers several advantages in comparison with radioisotopes. Firstly, they do not emit harmful radiation and can therefore be applied safely both in the laboratory and in the field. Secondly, the samples can be dried for safe storage and easy transportation. Thirdly, no aggressive chemicals are required for sample analysis.