Vanchrobactin: absolute configuration and total synthesis

The stereochemistry of vanchrobactin, a siderophore produced by the bacterial fish pathogenVibrio anguillarum serotype O2, was elucidated by chiral capillary electrophoresis analysis and total synthesis as N-[N′-(2,3-dihydroxybenzoyl)-d-arginyl]-l-serine.     

Structural characterization of vanchrobactin, a new catechol siderophore produced by the fish pathogen Vibrio anguillarum serotype O2

Vanchrobactin, a new catecol-type siderophore produced by cells of the fish pathogen Vibrio anguillarum serotype O2, has been isolated from the supernatants of iron-deficient cultures. Its structure was characterized from spectral data and established as N-[N′-(2,3-dihydroxybenzoyl)-arginyl]-serine.     

Lipopolysaccharides from Serratia marcescens possess one or two 4-amino-4-deoxy-L-arabinopyranose 1-phosphate residues in the lipid A and D-glycero-D-talo-oct-2-ulopyranosonic acid in the inner core region

The carbohydrate backbones of the core-lipid A region were characterized from the lipopolysaccharides (LPSs) of Serratia marcescens strains 111R (a rough mutant strain of serotype O29) and IFO 3735 (a smooth strain not serologically characterized but possessing the O-chain structure of serotype O19). The LPSs were degraded either by mild hydrazinolysis (de-O-acylation) and hot 4 M KOH (de-N-acylation), or by hydrolysis in 2 % aqueous acetic acid, or by deamination. Oligosaccharide phosphates were isolated by high-performance anion-exchange chromatography. Through the use of compositional analysis, electrospray ionization Fourier transform mass spectrometry, and 1H and 13C NMR spectroscopy applying various one- and two-dimensional experiments, we identified the structures of the carbohydrate backbones that contained D-glycero-D-talo-oct-2-ulopyranosonic acid and 4-amino-4-deoxy-L-arabinose 1-phosphate residues. We also identified some truncated structures for both strains. All sugars were D-configured pyranoses and alpha-linked, except where stated otherwise.     

Another Bacillus sphaericus serotype harbouring strains very toxic to mosquito larvae: Serotype H6

Ten isolates of Bacillus sphaericus from Ghana, very toxic to mosquito larvae, have been identified as belonging to serotype H6. These isolates can be represented by the head-group strain IAB59. They form crystals at the sporulation stage. Their larvicidal effect on Culex pipiens and Anopheles stephensi larvae is as high as that of the most toxic strains already known, e.g. 1593 and 2362 (serotype H5a,5b) and 2297 (serotype H25). Spore-crystal extracts of all these strains contain a 43-Kd polypeptide immunologically related to the 43-Kd polypeptide from strain 2362 described by other authors.     

Identification of a cluster of genes that directs desferrioxamine biosynthesis in Streptomyces coelicolor M145

Desferrioxamines are a structurally related family of tris-hydroxamate siderophores that form strong hexadentate complexes with ferric iron. Desferrioxamine B has been used clinically for the treatment of iron overload in man. We have unambiguously identified desferrioxamine E as the major desferrioxamine siderophore produced by Streptomyces coelicolor M145 and have identified a cluster of four genes (desA-D) that directs desferrioxamine biosynthesis in this model actinomycete. On the basis of comparative sequence analysis of the proteins encoded by these genes, we propose a plausible pathway for desferrioxamine biosynthesis. The desferrioxamine biosynthetic pathway belongs to a new and rapidly emerging family of pathways for siderophore biosynthesis, widely distributed across diverse species of bacteria, which is biochemically distinct from the better known nonribosomal peptide synthetase (NRPS) pathway used in many organisms for siderophore biosynthesis.     

Quantitatively resolving mixtures of isobaric compounds using chemical ionization mass spectrometry by modulating the reactant ion composition

Acrolein (C(3)H(4)O) and 1-butene (C(4)H(8)) can both be individually detected by proton transfer chemical ionization mass spectrometry (CI-MS). However, because these compounds are isobaric, mixtures of these two compounds cannot be resolved since both compounds react with H(3)O(+) via a proton-transfer reaction to form a protonated molecule that is detected at a nominal mass-to-charge ratio of 57 (m/z 57). While both compounds react with H(3)O(+) only acrolein reacts to any significant extent with H(3)O(+)(H(2)O). Recognizing that the electrical potential applied to a drift tube reaction mass spectrometer provides a simple and effective means for varying the relative intensity of the H(3)O(+) and H(3)O(+)(H(2)O) reactant ions we have developed a method whereby we make use of this reactivity difference to resolve mixtures of these two compounds. We demonstrate a technique where the individual contributions of acrolein and 1-butene within a mixture can be quantitatively resolved by systematically changing the reagent ion from H(3)O(+) to H(3)O(+)(H(2)O) through control of the electric potential applied to the drift tube reaction region of a proton transfer reaction mass spectrometer.     

Label-free detection of a bacterial pathogen using an immobilized siderophore, deferoxamine

Pathogenic bacteria obtain the iron necessary for survival by releasing an iron chelator, termed a siderophore, and retrieving the iron-siderophore complex via a cell surface siderophore receptor. We have exploited the high affinity of Yersinia enterocolitica for its siderophore, deferoxamine, to develop a rapid method for capture and identification of Yersinia. In this methodology, a deferoxamine-bovine serum albumin conjugate is printed onto a gold-plated chip in a parallel line pattern. After flowing a suspension of Yersinia across the siderophore-derivatized chip, any Yersinia that binds to the chip is detected by dark-field microscopy analysis of the scattered light, followed by Fourier transform analysis of the scattering pattern. Since peak intensities are found to correlate with pathogen concentration, pathogen titers as low as 10(3) cfu/ml can be readily detected. Moreover, immobilized deferoxamine can distinguish Y. enterocolitica, which binds ferrioxamine (deferoxamine-Fe), from Staphylococcus aureus, Mycobacterium smegmatis and Pseudomonas aeruginosa, which don't. Because human pathogens cannot easily mutate their iron retrieval systems without loss of viability, we suggest that few if any mutant Yersinia will emerge that can avoid detection. Together with previous results demonstrating selective capture of Pseudomonas aeruginosa by its immobilized siderophore (pyoverdin), these data suggest that pathogen-specific siderophores may constitute effective and immutable capture ligands for rapid detection and identification of their cognate pathogens.     

Production of Siderophores by an Apple Root-Associated Streptomyces ciscaucasicus Strain GS2 Using Chemical and Biological OSMAC Approaches

Apple Replant Disease (ARD) is a significant problem in apple orchards that causes root tissue damage, stunted plant growth, and decline in fruit quality, size, and overall yield. Dysbiosis of apple root-associated microbiome and selective richness of Streptomyces species in the rhizosphere typically concurs root impairment associated with ARD. However, possible roles of Streptomyces secondary metabolites within these observations remain unstudied. Therefore, we employed the One Strain Many Compounds (OSMAC) approach coupled to high-performance liquid chromatography-high-resolution tandem mass spectrometry (HPLC-HRMSⁿ) to evaluate the chemical ecology of an apple root-associated Streptomyces ciscaucasicus strain GS2, temporally over 14 days. The chemical OSMAC approach comprised cultivation media alterations using six different media compositions, which led to the biosynthesis of the iron-chelated siderophores, ferrioxamines. The biological OSMAC approach was concomitantly applied by dual-culture cultivation for microorganismal interactions with an endophytic Streptomyces pulveraceus strain ES16 and the pathogen Cylindrocarpon olidum. This led to the modulation of ferrioxamines produced and further triggered biosynthesis of the unchelated siderophores, desferrioxamines. The structures of the compounds were elucidated using HRMSⁿ and by comparison with the literature. We evaluated the dynamics of siderophore production under the combined influence of chemical and biological OSMAC triggers, temporally over 3, 7, and 14 days, to discern the strain’s siderophore-mediated chemical ecology. We discuss our results based on the plausible chemical implications of S. ciscaucasicus strain GS2 in the rhizosphere.     

A spectrophotometric method to determine the siderophore production by strains of fluorescent Pseudomonas in the presence of copper and iron

A simple procedure to determine levels of siderophore production by strains of Pseudomonas, particularly the Avm strain is described. Bacterial cells were incubated for 24 h in iron-rich (RM) and iron-limiting conditions (RM-Fe) with and without 6 and 60 μM of CuSO₄. Cells grown under iron-limiting conditions developed a green color even in the presence of Cu. The spent media supernatants from the Avm cells grown in RM-Fe medium showed a maximum peak of absorbance at 400 nm, which suggest that this strain produced a single type of siderophore. The presence of 60 μM of CuSO₄ in the cultures did not interfere with the detection of siderophores in the spent media. Clear supernatants obtained from cultures of 10 fluorescent Pseudomonas were diluted 1 to 10 in deionized water and the absorption at 400 nm was determined. The results demonstrated the clear discriminating capacity of this highly practical procedure to categorize a great number of fluorescent Pseudomonas strains by the range of siderophore production.     

Clustering structure of aqueous solution of kinetic inhibitor of gas hydrates

Poly-[N-vinylcaprolactam] (PVCAP) and its related compounds are specific polymeric compounds for inhibiting hydrate formation. To clarify the inhibition mechanism of these compounds on hydrate nucleation at the molecular level, we measured the mass spectra of clusters generated from the fragmentation of liquid droplets including N-methylcaprolactam (NMCAP; functional group of PVCAP). By comparing the mass spectra of clusters of the solutions--pure D2O, tetrahydrofuran (THF)-D2O, NMCAP-D2O, and THF-NMCAP-D2O--it was found that the interaction of NMCAP with D2O was much stronger than that of THF with D2O. The relative intensity ratio of D+(NMCAP)m(D2O)n clusters to all the clusters observed for the NMCAP-D2O (1:250) mixed solution was 0.45. On the other hand, the relative intensity ratio of D+(THF)1(D2O)n clusters to all the clusters observed for the THF-D2O (1:17) mixed solution was 0.15. In the case of the THF-NMCAP-D2O three-component mixed solution, the NMCAP-D2O interaction was more predominant than the THF-D2O interaction, even at a lower NMCAP concentration. NMCAP reduces free mobile water molecules around NMCAP, but THF does not. This correlates with the facts that THF forms its hydrate below the freezing point and that PVCAP works as an inhibitor of gas hydrates.     

Near edge X-ray absorption fine structure spectroscopy of bacterial hydroxamate siderophores in aqueous solutions

X-ray absorption spectroscopy (XAS) is widely used to explore the coordination environments and structures of metal complexes in aqueous solutions and disordered phases. Although soft-XAS studies on gaseous phases, solid phases and their interfaces have shown that XAS is a versatile tool in studying the functional group composition of organic molecules, the application of XAS to studying aqueous solutions is seriously limited because of experimental difficulties. In this report, using a modified synchrotron endstation geometry, we show how soft-XAS was used to study the changes in electronic states of reactive functional groups in a bacterial macromolecule, desferrioxamine B (desB, a hydroxamate siderophore) and its structural analogue (acetohydroxamic acid (aHa)). We collected C, N, and O near edge X-ray absorption fine structure (NEXAFS) spectra of these molecules in aqueous solutions and complemented their spectral interpretation with calculated X-ray spectra of "hydrated" aHa. The experimental spectra of desB are similar to those for aHa at the C, N, and O K-edges. In addition, the electronic transitions of amide and hydroxamate functional groups in the macromolecule can be distinguished from the N spectra. Small energy differences in the pi*(C=O)NO and the transitions at the C- and N-edges of aHa and desB indicate that the substituent attached to N in desB ((CH2)n) determines the electron density in the (C=O)NO core. As the solution pH increased, the pi*(C=O)NO transition of the hydroxamate group of these two molecules exhibit energy shifts at the C-, N-, and O-edges, which are consistent with increased electron delocalization in the (C=O)NO core of aHa (and desB), predicted from the calculations. The spectra of the aHa(H2O)3- anion also provide evidence for partial N-deprotonation at pH values usually attributed to an O-acid. These results indicate that soft-XAS is well suited for studying the electronic states of different functional groups in aqueous organic macromolecules.     

Oxygen exchange between (de)nitrification intermediates and H2O and its implications for source determination of NO3- and N2O: a review

Stable isotope analysis of oxygen (O) is increasingly used to determine the origin of nitrate (NO(3)-) and nitrous oxide (N(2)O) in the environment. The assumption underlying these studies is that the (18)O signature of NO(3)- and N(2)O provides information on the different O sources (O(2) and H(2)O) during the production of these compounds by various biochemical pathways. However, exchange of O atoms between H(2)O and intermediates of the (de)nitrification pathways may change the isotopic signal and thereby bias its interpretation for source determination. Chemical exchange of O between H(2)O and various nitrogenous oxides has been reported, but the probability and extent of its occurrence in terrestrial ecosystems remain unclear. Biochemical O exchange between H(2)O and nitrogenous oxides, NO(2)- in particular, has been reported for monocultures of many nitrifiers and denitrifiers that are abundant in nature, with exchange rates of up to 100%. Therefore, biochemical O exchange is likely to be important in most soil ecosystems, and should be taken into account in source determination studies. Failing to do so might lead to (i) an overestimation of nitrification as NO(3)- source, and (ii) an overestimation of nitrifier denitrification and nitrification-coupled denitrification as N(2)O production pathways. A method to quantify the rate and controls of biochemical O exchange in ecosystems is needed, and we argue this can only be done reliably with artificially enriched (18)O compounds. We conclude that in N source determination studies, the O isotopic signature of especially N(2)O should only be used with extreme caution.     

Speciation and biosynthetic variation in four dictyoceratid sponges and their cyanobacterial symbiont, Oscillatoria spongeliae

Four species of marine sponges (Phylum Porifera, Order Dictyoceratida), which contain the filamentous cyanobacterial symbiont Oscillatoria spongeliae, were collected from four locations in Palau. The halogenated natural products associated with the symbiont were characterized from each sample, revealing that each species contained either chlorinated peptides, brominated diphenyl ethers, or no halogenated compounds. Analysis of the host sponges and the symbionts indicated that each species of sponge contained a distinct strain of morphologically similar cyanobacteria. Although cospeciation may be present in this group, we have identified that at least one host switching event has occurred in this symbiosis. Only the strain of O. spongeliae in the sponge containing the chlorinated compounds possessed genes involved in the biosynthesis of chlorinated leucine precursors, indicating that the chemical variation observed in these animals has a genetic foundation.     

Chemical Synthesis and Immunological Evaluation of Helicobacter pylori Serotype O6 Tridecasaccharide O‐Antigen Containing a dd‐Heptoglycan

The development of glycoconjugate vaccines against Helicobacter pylori is challenging. An exact epitope of the H. pylori lipo‐polysaccharide (LPS) O‐antigens that contain Lewis determinant oligosaccharides and unique dd ‐heptoglycans has not yet been identified. Reported here is the first total synthesis of H. pylori serotype O6 tridecasaccharide O‐antigen containing a terminal Le^y tetrasaccharide, a unique α‐(1→3)‐, α‐(1→6)‐, and α‐(1→2)‐linked heptoglycan, and a β‐d ‐galactose connector, by an [(2×1)+(3+8)] assembly sequence. Seven oligosaccharides covering different portions of the entire O‐antigen were prepared for immunological investigations with a particular focus on elucidation of the roles of the dd ‐heptoglycan and Le^y tetrasaccharide. Glycan microarray analysis of sera from rabbits immunized with isolated serotype O6 LPS revealed a humoral immune response to the α‐(1→3)‐linked heptoglycan, a key motif for designing glycoconjugate vaccines for H. pylori serotype O6.     

Synthesis, solution behavior, thermal stability, and biological activity of an Fe(III) complex of an artificial siderophore with intramolecular hydrogen bonding networks

Previously, an artificial siderophore complex, the iron(III) complex with tris[2-[(N-acetyl-N-hydroxy)glycylamino]ethyl]amine (TAGE), was constructed in order to understand the effect of intramolecular hydrogen bonding interaction on the siderophore function, and its structural characterization in the solid state was reported (Inorg. Chem. 2001, 40, 190). In this paper, the solution behavior of the M(III)-TAGE (M = Fe, Ga) system has been investigated using (1)H NMR, UV-vis, and FAB mass spectroscopies in efforts to characterize the biological implication of hydrogen bonding networks between the amide hydrogens and coordinating aminohydroxy oxygens of the complex. The temperature dependence of (1)H NMR spectra for Ga(III) complex of TAGE indicates that hydrogen bonding networks are maintained in polar solvents such as DMSO-d(6) and D(2)O. The UV-vis spectra of the Fe(III)-TAGE system under various pH conditions have shown that TAGE forms a tris(hydroxamato)iron(III) complex in an aqueous solution in the pH range 4-8. By contrast, tris[2-[(N-acetyl-N-hydroxy)propylamido]ethyl]amine (TAPE; TAGE analogue that is difficult to form intramolecular hydrogen bonding networks), which has been synthesized as a comparison of TAGE, forms both of bis- and tris(hydroxamato)iron(III) complexes in the same pH range. Both the stability constants (log beta(FeTAGE) = 28.6; beta(FeTAGE) = [Fe(III)TAGE]/([Fe(3+)][TAGE(3)(-)])) and pM (-log[Fe(3+)]) value for Fe(III)TAGE (pM 25) are comparable to those of a natural siderophore ferrichrome (log beta = 29.1 and pM 25.2). The kinetic study of the TAGE-Fe(III) system has given the following rate constants: the rate of the ligand exchange reaction between Fe(III)TAGE and EDTA is 6.7 x 10(-4) s(-1), and the removal rates of iron from diferric bovine plasma transferrin by TAGE are 2.8 x 10(-2) and 6.0 x 10(-3) min(-1). These values are also comparable to those of a natural siderophore desferrioxamine B under the same conditions. In a biological activity experiment, TAGE has promoted the growth of the siderophore-auxotroph Gram-positive bacterium Microbacterium flavescens, suggesting that TAGE mimics the activity of ferrichrome. These results indicate that the artificial siderophore with intramolecular hydrogen bonding networks, TAGE, is a good structural and functional model for a natural ferrichrome.     

以含铬类水滑石型层状化合物为模板制备硫化物半导体纳米晶

采用类水滑石型混合金属氢氧化物(CdCr-LDH和ZnCdCr-LDH)为前驱体, 通过气-固反应方法, 制备了根植于层状氢氧化物层板中的硫化镉纳米晶和硫化镉/硫化锌复合纳米晶, 通过改变前驱体(CdCr-LDH)中镉和铬的摩尔比可以调控硫化镉纳米晶的粒径.     

Characterization of the side-on coordinated bissuperoxo complexes of aluminum FAl(O(2))(2), ClAl(O(2))(2), and BrAl(O(2))(2) with triplet electronic ground states: a combined matrix IR and quantum chemical study

Matrix isolation has been used to study the photolytically induced reaction of AlX (X = F, Cl, or Br) with O(2). The peroxo and bisperoxo compounds XAlO(2) and XAl(O(2))(2) are found to be the products of these reactions. While the peroxo species XAlO(2) were already addressed in a separate work, we concentrate herein on the bissuperoxo complexes XAl(O(2))(2), which are to our knowledge the first examples of such complexes with Al centers. Our IR spectroscopic results taking in the effect of isotopic substitution ((16)O/(18)O) allied with quantum chemical calculations show that the O(2) moieties in these complexes are side-on coordinated, leading to an overall C(2)(v)() symmetry of the complexes and a spin multiplicity of 3. The O-O distance of about 1.366 A argues for the presence of superoxide units. The force constants are, however, somewhat smaller than expected for a superoxide anion and indicate that the bonding in the complexes cannot be described simply on the basis of an ionic model. Interestingly a photoinduced intramolecular isotopic scrambling process is observed for the compounds resulting in partial conversion of the XAl((16)O(2))((18)O)(2) isotopomer into XAl((16)O(18)O)((16)O(18)O). The properties of the complexes will be compared to those of complexes to transition metal centers.     

Mixing and Matching Siderophore Clusters: Structure and Biosynthesis of Serratiochelins from Serratia sp. V4

Interrogation of the evolutionary history underlying the remarkable structures and biological activities of natural products has been complicated by not knowing the functions they have evolved to fulfill. Siderophores-soluble, low molecular weight compounds-have an easily understood and measured function: acquiring iron from the environment. Bacteria engage in a fierce competition to acquire iron, which rewards the production of siderophores that bind iron tightly and cannot be used or pirated by competitors. The structures and biosyntheses of "odd" siderophores can reveal the evolutionary strategy that led to their creation. We report a new Serratia strain that produces serratiochelin and an analog of serratiochelin. A genetic approach located the serratiochelin gene cluster, and targeted mutations in several genes implicated in serratiochelin biosynthesis were generated. Bioinformatic analyses and mutagenesis results demonstrate that genes from two well-known siderophore clusters, the Escherichia coli enterobactin cluster and the Vibrio cholera vibriobactin cluster, were shuffled to produce a new siderophore biosynthetic pathway. These results highlight how modular siderophore gene clusters can be mixed and matched during evolution to generate structural diversity in siderophores.     

硼合多羟基醇希土配合物的合成与性质及其配位作用的研究

本文合成了硼合甘油希土和硼合葡萄糖希土二类共八个配合物。用化学分析、红外光谱、紫外光谱及热谱确定其组成为:RE(BO_2·C_3H_8O_3)_3·nCH_3OH和RE(BO_2·C_6H_(12)O_6)_3·3H_2O(RE=Nd、Gd、Y、Yb)。摩尔电导测定表明这两类化合物均为中性配合物。红外光谱显示出硼与多羟基醇之间以硼氧四面体形式结合。本文还通过电位滴定法讨论了希土与硼合多羟基醇之间的配位作用。     

Zirconium-substituted isopolytungstates: structural models for zirconia-supported tungsten catalysts

The synthesis and characterization of a series of mixed W-Zr polynuclear Lindqvist-type complexes, deriving from hexatungstate [W6O19]2-, are described in this work. This family of compounds is built from {W5O18Zr}2- moieties as shown by the X-ray structures of the monomeric [W5O18Zr(H2O)(3-n)(DMSO)n]2- (n = 1 and 2) and dimeric [{W5O18Zr(mu-OH)}2]6- anions. A comprehensive spectroscopic study (183W NMR, FTIR, Raman, EXAFS, and EPR) of these compounds is presented. The goal of incorporating Zr(IV) cations into an oxotungstic core is to obtain spectroscopic models that could mimic the interactions that develop in supported catalysts between the active phase and the supporting oxide. This work tends to show that these molecular compounds can be regarded as soluble structural analogues of WOx/ZrO2 catalysts, which are interesting candidates for the skeletal isomerization of light n-alkanes.