Natural products from marine organisms and their associated microbes

The marine environment is distinguished by unique groups of organisms being the source of a wide array of fascinating structures. The enormous biodiversity of marine habitats is mirrored by the molecular diversity of secondary metabolites found in marine animals, plants and microbes. The recognition that many marine invertebrates contain endo- and epibiotic microorganisms and that some invertebrate-derived natural products are structurally related to bacterial metabolites suggests a microbial origin for some of these compounds. Other marine natural products, however, are clearly located in invertebrate tissue and microbial involvement in the biosynthetic process seems unlikely. The complexity of associations in marine organisms, especially in sponges, bryozoans and tunicates, makes it extremely difficult to definitively state the biosynthetic source of many marine natural products or to deduce their ecological significance. Whereas many symbiotic marine microorganisms cannot be isolated and cultured, numerous epi- and endobiotic marine fungi produce novel secondary metabolites in laboratory cultures. The potent biological activity of many marine natural products is of relevance for their ecological function but is also the basis of their biomedical importance.     

C-terminal modifications of a protein by UAG-encoded incorporation of puromycin during in vitro protein synthesis in the absence of release factor 1

Deactivation of release factor 1 by polyclonal antibodies in an in vitro translation system, which was used to express the esterase gene, led to the reversible elimination of naturally occurring termination. This technique allowed the antibiotic puromycin to be used as an acceptor substrate for the peptidyl residue in the peptidyl-transferase reaction. This resulted in more than 80 % yield of protein with C-terminally incorporated puromycin. pCpPuromycin that was either conjugated with the Cy3 fluorophor or biotin by N4 alkylation of cytosine, also acted as an acceptor substrate for the peptidyl-transferase reaction and was incorporated into the protein C terminus. The resulting conjugates possessed Cy3-specific fluorescence and affinity to streptavidin-coated surfaces, respectively. This left the enzymatic activity of the reporter protein unaffected. It was also shown that extension of puromycin on its 5'-hydroxyl end by up to ten deoxyoligonucleotides also allowed conjugation with the C terminus of in vitro translated protein when RF1-dependent termination was suppressed. However, the conjugation yield decreased upon addition of more than six nucleotides.     

Polyaza crown ethers as non-nucleosidic building blocks in DNA conjugates: synthesis and remarkable stabilization of dsDNA

The synthesis of amphiphilic polyaza crown ether monomers X (benzyl-substituted), Y (palmityl-substituted) and Z (cholesteryl-substituted) and their incorporation into oligonucleotides are described. Their effects on thermal duplex stability were investigated by UV melting curve analysis in different alkaline metal buffer solutions. Thermal-denaturation experiments showed remarkable stabilization of dsDNA by polyaza crown ether monomers when incorporated in opposite positions. The series of polyaza crown ether monomers (X, Y and Z) with different overall lipophilicities showed a trend of increased stability of the corresponding dsDNA with increasing lipophilicity of the polyaza crown ether monomer. Multiple incorporations of benzyl-substituted polyaza crown ether monomer X as dangling ends on both sides of dsDNA resulted in strongly increased stability of the corresponding duplex.     

A unique mechanism for methyl ester formation via an amide intermediate found in myxobacteria

Secondary metabolism involves a broad diversity of biochemical reactions that result in a wide variety of biologically active compounds. Terminal amide formation during the biosynthesis of the myxobacterial electron-transport inhibitor, myxothiazol, was analyzed by heterologous expression of the unique nonribosomal-peptide synthetase, MtaG, and incubation with a synthesized substrate mimic. These experiments provide evidence that the terminal amide is formed from a carrier protein-bound myxothiazol acid that is thioesterified to MtaF. This intermediate is transformed to an amide by extension with glycine and subsequent oxidative cleavage by MtaG. The final steps of melithiazol assembly involve a highly similar protein-bound intermediate (attached to MelF, a homologue of MtaF), which is transformed to an amide by MelG (homologue of MtaG). In this study, we also show that the amide moiety of myxothiazol A can be hydrolyzed in vivo to the formerly unknown free myxothiazol acid by heterologous expression of melJ in the myxothiazol producer Stigmatella aurantiaca DW4/3-1. The methyltransferase MelK can finally methylate the acid to give rise to the methyl ester, which is produced as the final product in the melithiazol A biosynthetic pathway. These experiments clarify the role of MelJ and MelK during melithiazol assembly.     

Cathodic reduction of acids in dimethylformamide on platinum

A linear correlation was shown to exist between the acidity and the cyclic voltammetric half-potential of the reduction of acids in DMF for carboxylic and N-acids in the pK_a range of 6-16. Chlorophenols are reduced at slightly lower potentials giving a separate parallel line. Applying the obtained equation and employing the same method to literature data in DMSO, the pK_a values for conjugate aids of DMF and DMSO can be calculated, showing DMSO·H⁺ to be more acidic (pK_a = 2.9) than DMF·H⁺ (pK_a = 5.7). The analysis of cyclovoltammetric data demonstrated that a CE mechanism operates in the reduction of strong acids, including the conjugate acid of DMF. Weaker acids are reduced by direct discharge or a mixed mechanism.     

Rapid production of micropatterned surfaces using a fluid dynamical instability

The continuous, high speed patterning of polyethylene films with a micron‐structured silicone coating was investigated in a roll coating process that did not depend on the use of prestructured tools. Thermally curable polydimethylsiloxane (PDMS) resin was rheologically modified by the addition of highly agglomerated, aerosol‐derived silica and resulted in a Herschel–Bulkley fluid. Application of the modified siloxane in a roll coating process resulted in a fluid dynamical instability at high capillary numbers promoting the spontaneous formation of randomly branched surface structures. The shear‐thinning properties of the nanoparticle‐doped PDMS resin were adjusted as to preserve the wet, structured coating during the following thermal curing step. The highly regular pattern was characterized in terms of averaged branch width and could be controlled from micro‐ to millimeter size by adjusting coating roll velocity and roll gap distance. The adhesive properties of the structured coating were compared to unstructured conventional silicone coatings by measuring the release force of pressure‐sensitive adhesives. For rubber‐based tape, the release force of patterned PDMS was reduced by a factor of up to eight if compared to smooth reference silicone. These ultra‐low adhesive coatings may find applications in packaging, food processing, and for covering sanitary surfaces, offering a cost‐effective alternative to conventional surface structuring methods. POLYM. ENG. SCI., 46:1541–1547, 2006. © 2006 Society of Plastics Engineers     

Supported gold clusters and cluster-based nanomaterials: characterization, stability and growth studies by in situ GISAXS under vacuum conditions and in the presence of hydrogen

This contribution is devoted to study of the thermal stability and growth of gold nanoparticles supported on SiO₂/Si(111) and Al₂O₃/SiO₂/Si(111) as a function of initial cluster size, support material and level of surface coverage. Experimental evidence for “flipping” of two dimensional cluster structures from vertical orientation to horizontal on the support is presented.     

Kinetic modeling of hemicellulose hydrolysis in the presence of homogeneous and heterogeneous catalysts

Kinetic models were developed for the hydrolysis of O‐acetyl‐galactoglucomannan (GGM), a hemicellulose appearing in coniferous trees. Homogeneous and heterogeneous acid catalysts hydrolyze GGM at about 90°C to the monomeric sugars galactose, glucose, and mannose. In the presence of homogeneous catalysts, such as HCl, H₂SO₄, oxalic acid, and trifluoroacetic acid, the hydrolysis process shows a regular kinetic behavior, while a prominent autocatalytic effect was observed in the presence of heterogeneous cation‐exchange catalysts, Amberlyst 15 and Smopex 101. The kinetic models proposed were based on the reactivities of the nonhydrolyzed sugar units and the increase of the rate constant (for heterogeneous catalysts) as the reaction progresses and the degree of polymerization decreases. General kinetic models were derived and special cases of them were considered in detail, by deriving analytical solutions for product distributions. The kinetic parameters, describing the autocatalytic effect were determined by nonlinear regression analysis. The kinetic model described very well the overall kinetics, as well as the product distribution in the hydrolysis of water soluble GGM by homogeneous and heterogeneous catalysts. The modelling principles developed in the work can be in principle applied to hydrolysis of similar hemicelluloses as well as starch and cellulose. © 2014 American Institute of Chemical Engineers AIChE J, 60: 1066–1077, 2014     

Rapid Determination of the Amino Acid Configuration of Xenotetrapeptide

An E. coli strain with deletions in five transaminases (ΔaspC ΔilvE ΔtyrB ΔavtA ΔybfQ) was constructed to be unable to degrade several amino acids. This strain was used as an expression host for the analysis of the amino acid configuration of nonribosomally synthesized peptides, including the novel peptide “xenotetrapeptide” from Xenorhabdus nematophila, by using a combination of labeling experiments and mass spectrometry. Additionally, the number of D ‐amino acids in the produced peptide was assigned following simple cultivation of the expression strain in D₂O.