Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli

Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.

The cellular level of O-antigen polymerase Wzy determines chain length regulation by WzzB and WzzpHS-2 in Shigella flexneri 2a

The lipopolysaccharide O antigen of Shigella flexneri 2a has two preferred chain lengths, a short (S-OAg) composed of an average of 17 repeated units and a very long (VL-OAg) of about 90 repeated units. These chain length distributions are controlled by the chromosomally encoded WzzB and the plasmid-encoded Wzz(pHS-2) proteins, respectively. In this study, genes wzzB, wzz(pHS-2) and wzy (encoding the O-antigen polymerase) were cloned under the control of arabinose- and rhamnose-inducible promoters to investigate the effect of varying their relative expression levels on O antigen polysaccharide chain length distribution. Controlled expression of the chain length regulators wzzB and wzz(pHS-2) revealed a dose-dependent production of each modal length. Increase in one mode resulted in a parallel decrease in the other, indicating that chain length regulators compete to control the degree of O antigen polymerization. Also, when expression of the wzy gene is low, S-OAg but not VL-OAg is produced. Production of VL-OAg requires high induction levels of wzy. Thus, the level of expression of wzy is critical in determining O antigen modal distribution. Western blot analyses of membrane proteins showed comparable high levels of the WzzB and Wzz(pHS-2) proteins, but very low levels of Wzy. In vivo cross-linking experiments and immunoprecipitation of membrane proteins did not detect any direct interaction between Wzy and WzzB, suggesting the possibility that these two proteins may not interact physically but rather by other means such as via translocated O antigen precursors.

Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis

The core oligosaccharide component of the lipopolysaccharide can be subdivided into inner and outer core regions. In Escherichia coli, the inner core consists of two 3-deoxy-d-manno-octulosonic acid and three glycero-manno-heptose residues. The HldE protein participates in the biosynthesis of ADP-glycero-manno-heptose precursors used in the assembly of the inner core. HldE comprises two functional domains: an N-terminal region with homology to the ribokinase superfamily (HldE1 domain) and a C-terminal region with homology to the cytidylyltransferase superfamily (HldE2 domain). We have employed the structure of the E. coli ribokinase as a template to model the HldE1 domain and predict critical amino acids required for enzyme activity. Mutation of these residues renders the protein inactive as determined in vivo by functional complementation analysis. However, these mutations did not affect the secondary or tertiary structure of purified HldE1, as judged by fluorescence spectroscopy and circular dichroism. Furthermore, in vivo coexpression of wild-type, chromosomally encoded HldE and mutant HldE1 proteins with amino acid substitutions in the predicted ATP binding site caused a dominant negative phenotype as revealed by increased bacterial sensitivity to novobiocin. Copurification experiments demonstrated that HldE and HldE1 form a complex in vivo. Gel filtration chromatography resulted in the detection of a dimer as the predominant form of the native HldE1 protein. Altogether, our data support the notions that the HldE functional unit is a dimer and that structural components present in each HldE1 monomer are required for enzymatic activity.

Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)

The O7-specific lipopolysaccharide (LPS) in strains of Escherichia coli consists of a repeating unit made of galactose, mannose, rhamnose, 4-acetamido-2,6-dideoxyglucose, and N-acetylglucosamine. We have recently cloned and characterized genetically the O7-specific LPS biosynthesis region (rfbEcO7) of the E. coli O7:K1 strain VW187 (C. L. Marolda, J. Welsh, L. Dafoe, and M. A. Valvano, J. Bacteriol. 172:3590-3599, 1990). In this study, we localized the gnd gene encoding gluconate-6-phosphate dehydrogenase at one end of the rfbEcO7 gene cluster and sequenced that end of the cluster. Three open reading frames (ORF) encoding polypeptides of 275, 464, and 453 amino acids were identified upstream of gndEcO7, all transcribed toward the gnd gene. ORF275 had 45% similarity at the protein level with ORF16.5, which occupies a similar position in the Salmonella enterica LT2 rfb region, and presumably encodes a nucleotide sugar transferase. The polypeptides encoded by ORFs 464 and 453 were expressed under the control of the ptac promoter and visualized in Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gels and by maxicell analysis. ORF464 expressed GDP-mannose pyrophosphorylase and ORF453 encoded a phosphomannomutase, the enzymes for the biosynthesis pathway of GDP-mannose, one of the nucleotide sugar precursors for the formation of the O7 repeating unit. They were designated rfbMEcO7 and rfbKEcO7, respectively. The RfbMEcO7 polypeptide was homologous to the corresponding protein in S. enterica LT2, XanB of Xanthomonas campestris, and AlgA of Pseudomonas aeruginosa, all GDP-mannose pyrophosphorylases. RfbKEcO7 was very similar to CpsG of S. enterica LT2, an enzyme presumably involved in the biosynthesis of the capsular polysaccharide colanic acid, but quite different from the corresponding RfbK protein of S. enterica LT2.

Antimicrobial peptides and alytesin are co-secreted from the venom of the Midwife toad, Alytes maurus (Alytidae, Anura): Implications for the evolution of frog skin defensive secretions

The skin secretions of frogs and toads (Anura) have long been a known source of a vast abundance of bioactive substances. In the past decade, transcriptome data of the granular glands of anuran skin has given new impetus to investigations of the putative constituent peptides. Alytes obstetricans was recently investigated and novel peptides with antimicrobial activity were isolated and functionally characterised. However, genetic data for the evolutionarily ancient lineage to which Alytes belongs (midwife toads; Alytidae) remains unavailable.

Here we present the first such genetic data for Alytidae, derived via the granular gland transcriptome of a closely-related species of midwife toad, Alytes maurus. First, we present nucleotide sequences of the entire peptide precursors for four novel antimicrobial peptides (AMPs). The two precursors resemble those from Bombinatoridae in both their structural architecture and amino acid sequence. Each precursor comprises two AMPs as tandem repeats, with a member of the alyteserin-1 family (alyteserin-1Ma: GFKEVLKADLGSLVKGIAAHVAN-NH2 or alyteserin-1Mb: GFKEVLKAGLGSLVKGIPAHVAN-NH2) followed by its corresponding member from the alyteserin-2 family (alyteserin-2Ma: FIGKLISAASGLLSHL-NH2 or alyteserin-2Mb: ILGAIIPLVSGLLSHL-NH2). Synthetic replicates of the four AMPs possessed minimal inhibitory concentrations (MICs) ranging from 9.5 to 300 µM, with the most potent being alyteserin-2Ma. Second, we also cloned the cDNA encoding an alytesin precursor, with the active alytesin exhibiting high sequence identity to bombesin-related peptides from other frogs. All putative mature peptide sequences were confirmed to be present in the skin secretion via LC/MS.

The close structural resemblance of the alyteserin genes that we isolated for A. maurus with those of Bombina provide independent molecular evidence for a close evolutionary relationship between these genera as well as more support for the convergent evolution of the AMP system within anurans. In contrast to the more evolutionarily conserved nature of neuropeptides (including alytesin, which we also isolated), the more variable nature of the AMP system together with the sporadic distribution of AMPs among anuran amphibians fuels in part our hypothesis that the latter system was co-opted secondarily to fulfil a function in the innate immune system, having originally evolved for defence against potential macropredators.

Effect of precursor on the performance of alumina for the dehydration of methanol to dimethyl ether

Dimethyl ether (DME) is amongst one of the most promising alternative, renewable and clean fuels being considered as a future energy carrier. In this study, the comparative catalytic performance of γ-Al2O3 prepared from two common precursors (aluminum nitrate (AN) and aluminum chloride (AC)) is presented. The impact of calcination temperature was evaluated in order to optimize both the precursor and pre-treatment conditions for the production of DME from methanol in a fixed bed reactor. The catalysts were characterized by TGA, XRD, BET and TPD-pyridine. Under reaction conditions where the temperature ranged from 180 °C to 300 °C with a WHSV = 12.1 h−1 it was found that all the catalysts prepared from AN(η-Al2O3) showed higher activity, at all calcination temperatures, than those prepared from AC(γ-Al2O3). In this study the optimum catalyst was produced from AN and calcined at 550 °C. This catalyst showed a high degree of stability and had double the activity of the commercial γ-Al2O3 or 87% of the activity of commercial ZSM-5(80) at 250 °C.

A more direct way to make catalysts: one-pot ligand-assisted aerobic stripping and electrodeposition of copper on graphite

Electrodeposition of metals onto conductive supports such as graphite potentially provides a lower-waste method to form heterogeneous catalysts than the standard methods such as wet impregnation. Copper electrodeposition onto pressed graphite disc electrodes was investigated from aqueous CuSO4-ethylenediamine solutions by chronoamperometry with scanning electron microscopy used to ascertain the particle sizes obtained by this method. The particle size was studied as a function of pH, CuSO4-ethylenediamine concentration, and electrodeposition time. It was observed that decreasing the pH, copper-ethylenediamine concentration and time each decreased the size of the copper particles observed, with the smallest obtained being around 5-20 nm. Furthermore, electroless aerobic oxidation of copper metal in the presence of ethylenediamine was successfully coupled with the electrodeposition in the same vessel. In this way, deposition was achieved sequentially on up to twenty different graphite discs using the same ethylenediamine solution, demonstrating the recyclability of the ligand. The materials thus prepared were shown to be catalytically active for the mineralisation of phenol by hydrogen peroxide. Overall, the results provide a proof-of-principle that by making use of aerobic oxidation coupled with electrochemical deposition, elemental base metals can be used directly as starting materials to form heterogeneous catalysts without the need to use metal salts as catalyst precursors.

Post-slaughter changes in ATP metabolites, Reducing and phosphorylated sugars in chicken meat

The formation of ATP breakdown products in chicken M. pectoralis major post-slaughter is reported. The concentrations of metabolites were followed in chicken breast throughout the carcass processing post-slaughter and during chilled storage. The concentration of glucose remains similar throughout the period whilst that of glucose-6-phosphate decreases linearly. Glucose and glucose-6-phosphate concentrations were inversely related to the pHu of the breast meat throughout chilled storage. Rapid post-mortem glycolysis and high pHu values suggest the occurrence of stress at and pre-slaughter. Whilst ATP, ADP and AMP were rapidly broken down, the concentration of IMP rose rapidly and remained high. Concentrations of inosine, ribose and hypoxanthine increased gradually post-slaughter but an initial increase in ribose phosphate was not sustained. Most of the potential ribose present in chicken meat, believed to be important for flavor formation, remains bound in the form of inosine and IMP. There is evidence that additional breakdown pathways for ribose and ribose-5-phosphate may deplete the concentrations of these precursors.

A filamentation instability for streaming cosmic rays

We demonstrate that cosmic rays form filamentary structures in the precursors of supernova remnant shocks due to their self-generated magnetic fields. The cosmic ray filamentation results in the growth of a long-wavelength instability, and naturally couples the rapid non-linear amplification on small scales to larger length-scales. Hybrid magnetohydrodynamics-particle simulations are performed to confirm the effect. The resulting large-scale magnetic field may facilitate the scattering of high-energy cosmic rays as required to accelerate protons beyond the knee in the cosmic ray spectrum at supernova remnant shocks. Filamentation far upstream of the shock may also assist in the escape of cosmic rays from the accelerator.

Chemoenzymatic synthesis of monocyclic arene oxides and arene hydrates from substituted benzene substrates

Enantiopure cis-dihydrodiol bacterial metabolites of substituted benzene substrates were used as precursors, in a chemoenzymatic synthesis of the corresponding benzene oxides and of a substituted oxepine, via dihydrobenzene oxide intermediates. A rapid total racemization of the substituted benzene 2,3-oxides was found to have occurred, via their oxepine valence tautomers, in accord with predictions and theoretical calculations. Reduction of a substituted arene oxide to yield a racemic arene hydrate was observed. Arene hydrates have also been synthesised, in enantiopure form, from the corresponding dihydroarene oxide or trans-bromoacetate precursors. Biotransformation of one arene hydrate enantiomer resulted in a toluene-dioxygenase catalysed cis-dihydroxylation to yield a benzene cis-triol metabolite.

Purification of a cathepsin L-like proteinase secreted by adult Fasciola hepatica

A cysteine proteinase released in vitro by Fasciola hepatica was purified to homogeneity by Sephacryl S-200 gel filtration chromatography followed by QAE-Sephadex chromatography. The purified enzyme resolves as a single band with an apparent molecular size of 27 kDa on reducing SDS-polyacrylamide gel electrophoresis; however, under non-reducing conditions it migrates as multiple bands, each with enzymatic activity, in the apparent molecular size range 60-90 kDa. The sequence of the first 20 N-terminal amino acids of the enzyme shows considerable homology with cathepsin L-like proteinases. Immunolocalisation studies revealed that the cathepsin L-like proteinase is concentrated within vesicles in the gut epithelial cells of liver fluke.

A cleavable network based on crosslinked star polymers containing acid-labile diacetal crosslinks: Synthesis, characterization and hydrolysis

A hydrolyzable model network comprising interconnected star polymers was prepared by the sequential group transfer polymerization of methyl methacrylate and the acid-labile diacetal-based dimethacrylate crosslinker bis[(2-methacryloyloxy)ethoxymethyl] ether. in contrast to other polymer networks previously synthesized by our group, all the branching points of this polymer network were found to hydrolyze under mildly acidic conditions, giving a linear copolymer with the theoretically expected molecular weight and composition. The ease of hydrolysis of this polymer network renders it a good candidate for use in the biomedical field. The characterization of the synthesized network, its linear and star polymer precursors and the hydrolysis products of the network and its precursors, by a variety of techniques, established the successful synthesis and hydrolysis of this well-defined polymer nanostructure.

Synthesis and characterization of amphiphilic star copolymers of 2-(dimethylamino) ethyl methacrylate and methyl methacrylate: Effects of architecture and composition

Six amphiphilic star copolymers comprising hydrophilic units of 2-(dimethylamino)ethyl methacrylate (DMAEMA) and hydrophobic units of methyl methacrylate (MMA) were prepared by the sequential group transfer polymerization (GTP) of the two comonomers and ethylene glycol dimethacrylate (EGDMA) cross-linker. Four star-block copolymers of different compositions, one miktoarm star, and one statistical copolymer star were synthesized. The molecular weights (MWs) and MW distributions of all the star copolymers and their linear homopolymer and copolymer precursors were characterized by gel permeation chromatography (GPC), while the compositions of the stars were determined by proton nuclear magnetic resonance (H-1 NMR) spectroscopy. Tetrahydrofuran (THF) solutions of all the star copolymers were characterized by static light scattering to determine the absolute weight-average MW ((M) over bar (w)) and the number of arms of the stars. The R, of the stars ranged between 359,000 and 565,000 g mol(-1), while their number of arms ranged between 39 and 120. The star copolymers were soluble in acidic water at pH 4 giving transparent or slightly opaque solutions, with the exception of the very hydrophobic DMAEMA(10)-b-MMA(30)-star, which gave a very opaque solution. Only the random copolymer star was completely dispersed in neutral water, giving a very opaque solution. The effective pKs of the copolymer stars were determined by hydrogen ion titration and were found to be in the range 6.5-7.6. The pHs of precipitation of the star copolymer solutions/dispersions were found to be between 8.8-10.1, except for the most hydrophobic DMA-EMA(10)-b-MMA(30)-Star, which gave a very opaque solution over the whole pH range. (c) 2006 Elsevier Ltd. All rights reserved.

Synthesis and characterization of star polymers and cross-linked star polymer model networks with cores based on an asymmetric, hydrolyzable dimethacrylate cross-linker

A hydrolyzable dimethacrylate cross-linker, 2-methyl-2,4-pentanediol dimethacrylate (MPDMA), was synhesized by the reaction of 2-methyl-2,4-pentanediol and methacryloyl chloride in the presence of triethylamine. This cross-linker was used to prepare a neat cross-linker network and three cross-linked star polymer model networks (CSPMNs) of methyl methacrylate (MMA), as well as star-shaped polymers of MMA, by group transfer polymerization (GTP). Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions (MWDs) of the linear polymer precursors, and demonstrated the increase in molecular weight (MW) on each successive addition of cross-linker or monomer. Characterization of the star polymers by static light scattering (SLS) in THF showed that star polymers with MPDMA cores bear a relatively small number of arms, between 7 and 35. All star polymers and polymer networks containing the MPDMA cross-linker were hydrolyzed at room temperature in neat trifluoroacetic acid to yield lower-MW products.

Synthesis and characterization of polymer networks and star polymers containing a novel, hydrolyzable acetal-based dimethacrylate cross-linker

An acid-labile dimethaerylate acetal cross-linker,di(methacryloyloxy-l-ethoxy)methane(DMOEM), was synthesized by the reaction of 2-hydroxyethyl methacrylate and paraformaldehyde using p-toluenesulfonic acid and toluene as catalyst and solvent, respectively. Group transfer polymerization was employed to use this cross-linker in the preparation of nine hydrolyzable polymer structures: one neat cross-linker network, one randomly cross-linked network of methyl methacrylate (MMA), and seven star-shaped polymers of MMA. Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions of the linear polymer precursors to the stars and demonstrated the increase in molecular weight upon the addition of cross-linker for the formation of star-shaped polymers. Characterization of the star polymers in THF using static light scattering and GPC showed that the molecular weights and the number of arms of each star polymer increased with an increase in the molar ratio of cross-linker to initiator and with a decrease in the molar ratio of monomer to initiator. The star polymers with DMOEM cores bore a smaller number of arms than those cross-linked with the non-hydrolyzable commercial cross-linker ethylene glycol dimethacrylate due to the bulkier structure of DMOEM. All DMOEM-containing polymer networks and star polymers were completely hydrolyzed within 48 h using hydrochloric acid in THF.