Discovery of a New, Recurrent Enzyme in Bacterial Phosphonate Degradation: (R)-1-Hydroxy-2-aminoethylphosphonate Ammonia-lyase.

Phosphonates represent an important source of bioavailable phosphorus in certain environments. Accordingly, many microorganisms (particularly marine bacteria) possess catabolic pathways to degrade these molecules. One example is the widespread hydrolytic route for the breakdown of 2-aminoethylphosphonate (AEP, the most common biogenic phosphonate). In this pathway, the aminotransferase PhnW initially converts AEP into phosphonoacetaldehyde (PAA), which is then cleaved by the hydrolase PhnX to yield acetaldehyde and phosphate. This work focuses on a pyridoxal 5'-phosphate-dependent enzyme that is encoded in >13% of the bacterial gene clusters containing the phnW-phnX combination. This enzyme (which we termed PbfA) is annotated as a transaminase, but there is no obvious need for an additional transamination reaction in the established AEP degradation pathway. We report here that PbfA from the marine bacterium Vibrio splendidus catalyzes an elimination reaction on the naturally occurring compound (R)-1-hydroxy-2-aminoethylphosphonate (R-HAEP). The reaction releases ammonia and generates PAA, which can be then hydrolyzed by PhnX. In contrast, PbfA is not active toward the S enantiomer of HAEP or other HAEP-related compounds such as ethanolamine and d,l-isoserine, indicating a very high substrate specificity. We also show that R-HAEP (despite being structurally similar to AEP) is not processed efficiently by the PhnW-PhnX couple in the absence of PbfA. In summary, the reaction catalyzed by PbfA serves to funnel R-HAEP into the hydrolytic pathway for AEP degradation, expanding the scope and the usefulness of the pathway itself.

Toxic metal sequential sequestration in water using new amido-aminoacid ligand as a model for the interaction with polyamidoamines.

Polyamidoamines are low cost and easily synthesized materials that may find applications in cations sequestration and water treatment. In this paper a new amido-aminoacid ligand containing methionine has been designed as a monomeric model of the corresponding polyamidoamine. The amido-aminoacid ligand has been synthesized in high yield, by reacting acrylamide and methionine via aza-Michael addition in water and mild temperature conditions. The reaction has been monitored by NMR and Raman spectroscopies and the crystal structure has been determined by X-ray diffraction analysis. The coordination ability of the ligand towards Cu2+ cations in water, as well as its affinity for Ni2+ and Co2+ has been studied by potentiometric and spectrophotometric techniques. The divalent metal cations sequestration from water may occur with sequential selection by changing the pH of the solution. The copper complex with two coordinated ligands has been fully characterized in the solid state by single crystal X-ray diffraction. The results are discussed with a view to use these materials in the treatment of water contaminated by toxic transition metal ions.

Birth of a pathway for sulfur metabolism in early amniote evolution.

Among amniotes, reptiles and mammals are differently adapted to terrestrial life. It is generally appreciated that terrestrialization required adaptive changes of vertebrate metabolism, particularly in the mode of nitrogen excretion. However, the current paradigm is that metabolic adaptation to life on land did not involve synthesis of enzymatic pathways de novo, but rather repurposing of existing ones. Here, by comparing the inventory of pyridoxal 5'-phosphate-dependent enzymes in different amniotes, we identify in silico a pathway for sulfur metabolism present in chick embryos but not in mammals. Cysteine lyase contains haem and pyridoxal 5'-phosphate co-factors and converts cysteine and sulfite into cysteic acid and hydrogen sulfide, respectively. A specific cysteic acid decarboxylase produces taurine, while hydrogen sulfide is recycled into cysteine by cystathionine beta-synthase. This reaction sequence enables the formation of sulfonated amino acids during embryo development in the egg at no cost of reduced sulfur. The pathway originated around 300 million years ago in a proto-reptile by cystathionine beta-synthase duplication, cysteine lyase neofunctionalization and cysteic acid decarboxylase co-option. Our findings indicate that adaptation to terrestrial life involved innovations in metabolic pathways, and reveal the molecular mechanisms by which such innovations arose in amniote evolution.

A community-built calibration system: The case study of quantification of metabolites in grape juice by qNMR spectroscopy.

Nuclear Magnetic Resonance (NMR) is an analytical technique extensively used in almost every chemical laboratory for structural identification. This technique provides statistically equivalent signals in spite of using spectrometer with different hardware features and is successfully used for the traceability and quantification of analytes in food samples. Nevertheless, to date only a few internationally agreed guidelines have been reported on the use of NMR for quantitative analysis. The main goal of the present study is to provide a methodological pipeline to assess the reproducibility of NMR data produced for a given matrix by spectrometers from different manufacturers, with different magnetic field strengths, age and hardware configurations. The results have been analyzed through a sequence of chemometric tests to generate a community-built calibration system which was used to verify the performance of the spectrometers and the reproducibility of the predicted sample concentrations.

Nuclear Magnetic Resonance of Gangliosides.

Structure, conformation, and dynamics of sphingolipids can provide substantial help in better understanding sphingolipid-ligand interaction mechanisms. Both the oligosaccharide structure and the ceramide moiety of native glycosphingolipid can be established directly by NMR spectroscopic analysis without the necessity to resort to any other chemical or spectroscopic methods. NMR is a powerful technique to investigate interaction between small ligand, such as ganglioside, and membrane protein.

Performance Assessment in Fingerprinting and Multi Component Quantitative NMR Analyses.

An interlaboratory comparison (ILC) was organized with the aim to set up quality control indicators suitable for multicomponent quantitative analysis by nuclear magnetic resonance (NMR) spectroscopy. A total of 36 NMR data sets (corresponding to 1260 NMR spectra) were produced by 30 participants using 34 NMR spectrometers. The calibration line method was chosen for the quantification of a five-component model mixture. Results show that quantitative NMR is a robust quantification tool and that 26 out of 36 data sets resulted in statistically equivalent calibration lines for all considered NMR signals. The performance of each laboratory was assessed by means of a new performance index (named Qp-score) which is related to the difference between the experimental and the consensus values of the slope of the calibration lines. Laboratories endowed with a Qp-score falling within the suitable acceptability range are qualified to produce NMR spectra that can be considered statistically equivalent in terms of relative intensities of the signals. In addition, the specific response of nuclei to the experimental excitation/relaxation conditions was addressed by means of the parameter named NR. NR is related to the difference between the theoretical and the consensus slopes of the calibration lines and is specific for each signal produced by a well-defined set of acquisition parameters.

Application of 1H NMR for the characterisation of cocoa beans of different geographical origins and fermentation levels.

This study reports for the first time the use of (1)H NMR technique combined with chemometrics to study the metabolic profile of cocoa (Theobroma cacao L.) beans of different varieties, origin and fermentation levels. Results of PCA applied to cocoa bean (1)H NMR dataset showed that the main factor influencing the cocoa bean metabolic profile is the fermentation level. In fact well fermented brown beans form a group clearly separated from unfermented, slaty, and underfermented, violet, beans, independently of the variety or geographical origin. Considering only well fermented beans, the metabolic profile obtained by (1)H NMR permitted to discriminate between some classes of samples. The National cocoa of Ecuador, known as Arriba, showed the most peculiar characteristics, while the samples coming from the African region showed some similar traits. The dataset obtained, representative of all the classes of soluble compounds of cocoa, was therefore useful to characterise fermented cocoa beans as a function of their origin and fermentation level.

Application of ¹H NMR for the characterisation and authentication of ''Tonda Gentile Trilobata" hazelnuts from Piedmont (Italy).

The Italian hazelnut (Corylus avellana L.) cultivar "Tonda Gentile Trilobata" (TGT) is covered by protected geographical indication "Nocciola Piemonte" and is well-known as the best-suited hazelnut for the industrial transformation into roasted kernel. The hazelnut cultivar identification is primarily based on morphological characteristics, so there is the need for more objective analytical methods for high quality hazelnut authentication. This study reports the (1)H NMR fingerprinting of raw and roasted hazelnut, with the aim of obtaining hazelnut classification based on their spectroscopic pattern. (1)H NMR analyses were carried out on polar extracts of TGT and other cultivars: the data were analysed with multivariate statistical methods. Results showed that (1)H NMR combined with chemometrics is useful to characterise the hazelnuts as a function of the cultivars, both on raw and roasted form. The classification models allowed identifying molecular markers useful to distinguish TGT from other types, among these trigonelline, amino acids and an unidentified orto-disubstituted aromatic compound.

1H NMR study of fermented cocoa (Theobroma cacao L.) beans.

This study reports for the first time the metabolic profile of cocoa (Theobroma cacao L.) beans using the (1)H NMR technique applied to polar extracts of fermented cocoa beans. The simultaneous detection and quantification of amino acids, polyalcohols, organic acids, sugars, methylxanthines, catechins, and phenols were obtained by assigning the major signals of the spectra for different varieties of cocoa beans (Forastero, Criollo, and Trinitario) from different countries (Ecuador, Ghana, Grenada, and Trinidad). The data set obtained, representative of all classes of soluble compounds of cocoa, was useful to characterize the fermented cocoa beans as a function of the variety and geographic origin.

NMR analysis of a series of imidazobenzoxazines.

The complete (1)H and (13)C NMR assignment of a series of imidazobenzoxazines by a combination of one- and two-dimensional experiments (COSY, HSQC and HMBC) is studied. Moreover, 2D NOESY and 1D selective NOESY are reported. This procedure allows the identification of the regioisomers obtained.

Complete 1H and 13C NMR spectral assignment of benzo[d]isothiazole derivatives and of an isoindole isoster.

The complete (1)H and (13)C NMR assignments of the novel compound methyl 2-amino-3-(benzo[d]isothiazol-3-yl)propanoate (1), of 3-amino-5-methylbenzo[d]isothiazole (2) and N-(t-butyloxycarbonyl)-2-aminobenzo[d]isothiazol-3(2H)-one (3) and of the desulfurated isostere of 3, N-(t-butyloxycarbonyl)-2-aminoisoindolin-1-one (4), using 1D and 2D NMR techniques, including COSY, INADEQUATE, HSQC, and HMBC experiments are reported.

Reactivity of Ph2P(Se)CH2C6H4CH2P(Se)Ph2 with [M3(CO)12] (M=Ru or Fe). Synthesis and characterization of the new carbene cluster [Ru3(mu3-Se)(mu3-H)(mu2-PPh2)(CO)6(mu2-CHC6H4CH2PPh2)].

The reactions of [M3(CO)12] (M=Ru or Fe) with 1,2 bis[(diphenylphosphino)methyl]benzene diselenide (dpmbSe2) in hot toluene afford a variety of phosphine-substituted selenido carbonyl clusters. They belong to the following three families: (i) 50-electron clusters with a M3Se2 core (2, 3, 5-7), (ii) 48-electron clusters with a M3Se core (1, 8), (iii) 34-electron clusters with a M2Se2 core (4). All these species derive from the P=Se bond cleavage. Cluster 1, which contains a hydrido, a phosphido, and a carbene ligand, is produced by multiple fragmentation of the diphosphine. This fragmentation appears related to the presence of the selenido ligand on the cluster, as the reaction of [Ru3(CO)12] with dpmb (not selenized) produces only carbonyl substitution by the phosphine to give [Ru3(CO)10(mu-dpmb)] (9). All the clusters synthesized have been characterized by spectroscopic techniques, and in some cases fluxional behavior has been detected in solution by NMR analysis. The structures of 1, 2, and 7-9 have been determined by X-ray diffraction methods.

Variable strategy toward carbasugars and relatives. 4. Viable access to (4a-carbapentofuranosyl)amines, (5a-carbahexopyranosyl)amines, and amino acids thereof.

A chiral, divergent synthesis of two carbafuranosylamines, 1 and 2, two carbapyranosylamines, 3 and 4, two carbafuranosylamino acids, 5 and 6, and two carbapyranosylamino acids, 7 and 8, has been achieved. Highlights of the procedure include the following: a diastereoselective crossed vinylogous Mukaiyama aldol coupling between N-(tert-butoxycarbonyl)-2-[(tert-butyldimethylsilyl)oxy]pyrrole (TBSOP, 9) and 2,3-O-isopropylidene-D-glyceraldehyde (10) for the assembly of the target compound carbon backbone; a high-yielding silylative cycloaldolization that gives the cyclopentanoid and cyclohexanoid motifs; and a reductive or hydrolytic breakage of the lactam C(O)-N link to liberate the carbasugar and install the desired pseudo-anomeric amine and the hydroxymethyl or carboxyl functionalities. The sequences leading to trans-configured carbafuranosyl compounds 1 and 5 and carbapyranosyl compounds 3 and 7 were 12- and 13-step processes, with overall yields of 34%, 35%, 17%, and 16%. Cis-configured isomers 2, 4, 6, and 8 were obtained only in minor yields.