Processing of artificial peptide-DNA-conjugates by the mitochondrial intermediate peptidase (MIP).

Import of DNA from the cytoplasm into the mitochondrial matrix is an obligatory step for an in organello site-directed mutagenesis or gene therapy approach on mitochondrial DNA diseases. In this context, we have developed an artificial DNA translocation vector that is composed of the mitochondrial signal peptide of the ornithine transcarbamylase (OTC) and a DNA moiety. While this vector is capable of directing attached passenger molecules to the mitochondrial matrix, the recognition of this artificial molecule by the endogenous mitochondrial signal peptide processing machinery as well as the cleavage of the peptide plays a pivotal role in the release of the attached DNA. To study the proteolytic processing of the artificial vector, various signal peptide-DNA-conjugates were treated with purified mitochondrial intermediate peptidase. When the leader peptide is directly linked to the DNA moiety without an intervening spacer, MIP processing is prevented. Cleavage of the peptide can be restored, however, when the first ten amino acid residues of the mature part of OTC are appended at the carboxy-terminal end of the signal peptide. Our results show that artificial peptide-DNA-conjugates are recognized by the mitochondrial proteolytic machinery, and therefore an interference of the peptide with the DNA function can be excluded.     

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

Background  

In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously.     

Towards tailor-made oligosaccharides—chemo-enzymatic approaches by enzyme and substrate engineering

Carbohydrate structures have been identified in eukaryotic and prokaryotic cells as glycoconjugates with communication skills. Their recently discussed role in various diseases has attracted high attention in the development of simple and convenient methods for oligosaccharide synthesis. In this review, recent approaches combining nature’s power for the design of tailor made biocatalysts by enzyme engineering and substrate engineering will be presented. These strategies lead to highly efficient and selective glycosylation reactions. The introduced concept shall be a first step in the direction to a glycosylation toolbox which paves the way for the tailor-made synthesis of designed carbohydrate structures.     

Glycosylation with activated sugars using glycosyltransferases and transglycosidases

The growing recognition of the roles of carbohydrates in fundamental biological processes and their potential application as functional foods and new therapeutics have generated a requirement for the general availability of larger amounts of varying carbohydrate structures.

Thus the synthesis of oligo-, polysaccharides and glycosylated substances/products represents a major challenge.

Activated sugars are key substrates for synthesis and glycosylation. Nucleotide activated sugars are natural tools for highly selective synthesis, providing complex polysaccharides, glycopeptides, glycolipids etc. However their high cost and availability limit their application. Sucrose acts as an activated substrate for a range of sucrase enzymes elaborating natural polysacchrides of the glucan and fructan type, which also serve for the synthesis and technical production of different oligosaccharides. Sucrose analogues have been shown to extend the range of oligosaccharide synthesis making new structures available incorporating further monosaccharides, such as mannose, galactose, xylose, rhamnose and fucose. A short overview of the use of glycosyl phosphates and glycosyl fluorides as substrates is also given.     

The gene encoding polyneuridine aldehyde esterase of monoterpenoid indole alkaloid biosynthesis in plants is an ortholog of the alpha/betahydrolase super family.

The biosynthesis of the anti-arrhythmic alkaloid ajmaline is catalysed by more than 10 specific enzymes. In this multistep process polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. PNAE was purified from cell suspension cultures of Rauvolfia serpentina. The N-terminal sequence and endoproteinase LysC fragments of the purified protein were used for primer design and for the amplification of specific PCR products leading to the isolation of PNAE-encoding cDNA from a R. serpentina library. The PNAE cDNA was fused with a C-terminal His-tag, expressed in Escherichia coli and purified to homogeneity using Ni-affinity chromatography. The pure enzyme shows extraordinary substrate specificity, completely different to other esterases. Sequence alignments indicate that PNAE is a new member of the alpha/beta hydrolase super family.     

Tight control of mitochondrial membrane potential by cytochrome c oxidase

In the present work we have critically examined the use of the KCN-titration technique in the study of the control of the cellular respiration by cytochrome c oxidase (COX) in the presence of the mitochondrial membrane potential (Δψ(mito)) in HepG2 cells. We clearly show that the apparent high inhibition threshold of COX in the presence of maximal Δψ(mito) is due to the KCN-induced decrease of Δψ(mito) and not to a low control of COX on the mitochondrial respiration. The tight control exerted by COX on the Δψ(mito) provides further insights for understanding the pathogenetic mechanisms associated with mitochondrial defects in human neuromuscular degenerative disorders.     

Polysaccharide synthesis of the levansucrase SacB from Bacillus megaterium is controlled by distinct surface motifs

Despite the widespread biological function of carbohydrates, the polysaccharide synthesis mechanisms of glycosyltransferases remain largely unexplored. Bacterial levansucrases (glycoside hydrolase family 68) synthesize high molecular weight, β-(2,6)-linked levan from sucrose by transfer of fructosyl units. The kinetic and biochemical characterization of Bacillus megaterium levansucrase SacB variants Y247A, Y247W, N252A, D257A, and K373A reveal novel surface motifs remote from the sucrose binding site with distinct influence on the polysaccharide product spectrum. The wild type activity (k(cat)) and substrate affinity (K(m)) are maintained. The structures of the SacB variants reveal clearly distinguishable subsites for polysaccharide synthesis as well as an intact active site architecture. These results lead to a new understanding of polysaccharide synthesis mechanisms. The identified surface motifs are discussed in the context of related glycosyltransferases.     

External compression increases forearm perfusion.

Application of compression stockings to the lower extremities is a widely used therapeutic intervention to improve venous return, but there is little information about the effects of compression on local arterial perfusion. Therefore, we tested the hypothesis that a positive external pressure increases forearm perfusion. The relation of increasing external pressure induced by standardized compression to the arterial inflow and arterial flow reserve of the forearm was critically evaluated in a group of healthy young men (n = 9). Flow was measured with venous occlusion plethysmography after a 10-min application of six different stockings with compression pressure increasing from 13 to 23 mmHg. During compression, the arterial inflow increased significantly from 3.7 +/- 0.85 to 8.8 +/- 2.01 ml.min(-1).100 ml tissue(-1) (P < 0.001) and the arterial flow reserve increased from 17.7 +/- 4.7 to 28.3 +/- 7.0 ml.min(-1).100 ml tissue(-1). The flow increase was persistent after 3 h of constant application of external pressure and also during simultaneous low-intensity hand grip. Similar results obtained with occlusion plethysmography were seen with MRI. During the interventions, forearm temperature was unchanged, and the volunteers reported no discomfort. In conclusion, 1) arterial perfusion of the human forearm increases more than twofold during application of external compression over a pressure range of 13-23 mmHg, and 2) the result is interpreted as an autoregulatory response following the decrease of the vascular transmural pressure gradient.