Characterization of the TDP-D-ravidosamine biosynthetic pathway: one-pot enzymatic synthesis of TDP-D-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate

Ravidomycin V and related compounds, e.g., FE35A-B, exhibit potent anticancer activities against various cancer cell lines in the presence of visible light. The amino sugar moieties (D-ravidosamine and its analogues, respectively) in these molecules contribute to the higher potencies of ravidomycin and analogues when compared to closely related compounds with neutral or branched sugars. Within the ravidomycin V biosynthetic gene cluster, five putative genes encoding NDP-D-ravidosamine biosynthetic enzymes were identified. Through the activities of the isolated enzymes in vitro, it is demonstrated that ravD, ravE, ravIM, ravAMT and ravNMT encode TDP-D-glucose synthase, TDP-4-keto-6-deoxy-D-glucose-4,6-dehydratase, TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase, TDP-3-keto-6-deoxy-D-galactose-3-aminotransferase, and TDP-3-amino-3,6-dideoxy-D-galactose-N,N-dimethyl-transferase, respectively. A protocol for a one-pot enzymatic synthesis of TDP-D-ravidosamine has been developed. The results presented here now set the stage to produce TDP-D-ravidosamine routinely for glycosylation studies.     

The sporothriolides. A new biosynthetic family of fungal secondary metabolites

The biosynthetic gene cluster of the antifungal metabolite sporothriolide 1 was identified from three producing ascomycetes: Hypomontagnella monticulosa MUCL 54604, H. spongiphila CLL 205 and H. submonticulosa DAOMC 242471. A transformation protocol was established, and genes encoding a fatty acid synthase subunit and a citrate synthase were simultaneously knocked out which led to loss of sporothriolide and sporochartine production. In vitro reactions showed that the sporochartines are derived from non-enzymatic Diels–Alder cycloaddition of 1 and trienylfuranol A 7 during the fermentation and extraction process. Heterologous expression of the spo genes in Aspergillus oryzae then led to the production of intermediates and shunts and delineation of a new fungal biosynthetic pathway originating in fatty acid biosynthesis. Finally, a hydrolase was revealed by in vitro studies likely contributing towards self-resistance of the producer organism.

A new family of fungal biosynthetic pathways is elucidated based on the use of fatty acid and citrate-like intermediates.

Gamma-lactone and alkyl citrate compounds derived from oxaloacetate are widespread natural products in fungi and often possess potent biological activities. Examples include sporothriolide 1,^1,2 piliformic acid 2,³ tyromycin 3⁴ and the cyclic maleidrides including byssochlamic acid 4^5,6 among others (Fig. 1). In some cases, for example those of 4 and squalestatin S1 5,⁷ detailed molecular studies have revealed that a dedicated polyketide synthase (PKS) produces a carbon skeleton that is then condensed with oxaloacetate by a citrate synthase (CS) to give an early alkyl citrate intermediate that is further oxidatively processed. In other cases, such as 1 and the sporochartines 6, the biosynthetic pathways are not yet clear.Open in a separate windowFig. 1Structures of γ-lactone and alkyl citrate metabolites from fungi. Bold bonds show oxaloacetate-derived carbons where known.Sporochartines 6a–6d^8,9 from the fungus Hypoxylon monticulosum CLL 205 (now referred to as Hypomontagnella spongiphila)¹⁰ possesses potent cytotoxicity (IC₅₀: 7.2 to 21.5 μM) vs. human cancer cell lines and are proposed to be Diels Alder (DA) adducts of the furofurandione sporothriolide 1, itself a potent antifungal agent (EC₅₀: 11.6 ± 0.8 μM),¹¹ and trienylfuranol A 7,¹² originally obtained from an endophytic fungus Hypoxylon submonticulosum DAOMC 242471 (now referred to as Hypomontagnella submonticulosa).¹³ Since the biosynthesis of sporothriolide 1 and related compounds is unknown, and biological DA reactions in fungi are currently of high interest,¹⁴ we decided to examine the biosynthesis of the sporochartines 6 in the Hypomontagnella spp. strains MUCL 54604 and CLL 205 (ref. 10 and 13) in detail.     

A two-stage one-pot enzymatic synthesis of TDP-L-mycarose from thymidine and glucose-1-phosphate

This report describes a procedure combining six enzymes native to Escherichia coli or Salmonella typhi, such as thymidine kinase (TK), thymidylate kinase (TMK), nucleoside diphosphate kinase (NDK), pyruvate kinase (PK; for ATP regeneration), TDP-glucose synthetase (RfbA), and TDP-glucose 4,6-dehydratase (RfbB), with five enzymes from Streptomyces fradiae, such as TylX3, TylC1, TylC3, TylK, and TylC2, that resulted in the biosynthesis of TDP-l-mycarose from glucose-1-phosphate and thymidine. This two-stage one-pot approach can be readily applied to the synthesis of other unusual sugars.     

Bamboo borer dust as a rich source of glucose-1-phosphate

Chemical characterization of bamboo borer dust (BBD) indicated that it contained 2.5 ±0.5% of an organic entity that was a watersoluble, acid-labile phosphate, nonreducing sugar with a retention period of 5.2 min on a sugar pack column during high pressure liquid chromatography (HPLC). It was subsequently identified and confirmed as glucose-1-phosphate (G-l-P) from its response to phosphoglucomutase and glucose-6-phosphatase treatment. Although the presence of G-l-P in such a large quantity in BBD is inexplicable, it provides a rare and rich source of G-l-P, making it a potential starting material for its isolation in pure state.     

Synthesis and evaluation of glucosamine-6-phosphate analogues as activators of glmS riboswitch

The glmS riboswitch is a ribozyme found in numerous Gram-positive bacteria and responds to the cellular concentrations of glucosamine 6-phosphate (GlcN6P). Given the importance of GlcN6P for cell wall biosynthesis, the glmS riboswitch has become a new drug target for the development of antibiotics. Herein, we describe the efficient synthesis of three GlcN6P analogues and their evaluation on inducing self-cleavage of the glmS riboswitch from Bacillus subtilis. Our results provide valuable information for further elucidation of the structure-activity relationships and drug design for glmS riboswitch antibiotics.     

The orthosomycins,a new family of antibiotics

A new family of antibiotics, the orthosomycins, which contain in their structures one or more orthoester linkages associated with carbohydrate residues, is described. Examples of orthosomycin antibiotics include flambamycin (1), the everninomicins -B2a, -C2b, -D2c and -2(3), hygromycin B4a, the destomycins -A4b, -B5 and -C4c, the antibiotics SS-56-C4d, A-396-I4e and, more recently, the avilamycins -A49a and -C49b. The structural elucidation of these orthosomycin antibiotics is discussed, with emphasis on structural similarities and differences, together with a commentary on their biological activities and structure-activity relationships.     

Efficient hydrolysis of glucose-1-phosphate catalyzed by metallomicelles with histidine residue

Phosphate esters play an important role in genetic information transfer, cell signal transduction, energy transmission and metabolic processes of living beings. Efficient catalytic hydrolysis of phosphate esters is still an attractive and challenging problem. Here, a new 2-amino-N-dodecyl-3-(1H-imidazol-5-yl)propanamide (L²) surfactant was synthesized and its metallomicelles of La³⁺, Cu²⁺, Co²⁺, and Zn²⁺ complexes were used as mimic metalloenzymes to catalyze the hydrolysis of glucose-1-phosphate (G1P) in a buffer solution at 35°C. The metallomicelle systems can efficiently catalyze the hydrolysis of G1P. The rare-earth metallomicelle LaL² has the highest catalytic activity compared with those of the transition metal micelles CuL², CoL², and ZnL². Different association behaviors of metallomicelles and substrate G1P were proposed. The imidazole group might accelerate the hydrolysis by activating H₂O associated with the metal into a metal-OH^? group. A possible catalytic mechanism was also discussed.     

Engineering biosynthetic pathways for deoxysugars: branched-chain sugar pathways and derivatives from the antitumor tetracenomycin

Sugar biosynthesis cassette genes have been used to construct plasmids directing the biosynthesis of branched-chain deoxysugars: pFL942 (NDP-L-mycarose), pFL947 (NDP-4-deacetyl-L-chromose B), and pFL946/pFL954 (NDP-2,3,4-tridemethyl-L-nogalose). Expression of pFL942 and pFL947 in S. lividans 16F4, which harbors genes for elloramycinone biosynthesis and the flexible ElmGT glycosyltransferase of the elloramycin biosynthetic pathway, led to the formation of two compounds: 8-alpha-L-mycarosyl-elloramycinone and 8-demethyl-8-(4-deacetyl)-alpha-L-chromosyl-tetracenomycin C, respectively. Expression of pFL946 or pFL954 failed to produce detectable amounts of a novel glycosylated tetracenomycin derivative. Formation of these two compounds represents examples of the sugar cosubstrate flexibility of the ElmGT glycosyltransferase. The use of these cassette plasmids also provided insights into the substrate flexibility of deoxysugar biosynthesis enzymes as the C-methyltransferases EryBIII and MtmC, the epimerases OleL and EryBVII, and the 4-ketoreductases EryBIV and OleU.     

Monitoring enzyme-catalyzed production of glucosamine-6P by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new enzymatic assay for glucosamine-6P synthase

A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) method for quantification of D-glucosamine-6P (GlcN-6P) that allows the kinetic study of glucosamine-6P synthase (Glms) is presented. The present report describes the optimization of the different steps of a new enzymatic assay for Glms based on in situ N-acetylation of GlcN-6P and MALDI-TOFMS analysis using N-(13C2)acetylglucosamine-6P as internal standard. Since no isotopically substituted GlcN-6P was available, the N-(13C2)acetyl derivative, easily obtained from (13C4)-acetic anhydride, was used as internal standard. Validation of the assay was achieved by measuring the fructose-6P Michaelis constant, in full agreement with reported values, and by studying the inhibition properties of arabinose-5P oxime.     

A highly efficient synthesis of [1-C, O]- and [1-C, H2]-glycerol for the elucidation of biosynthetic pathways

Labeled glycerol is a widely used biochemical probe to investigate biosynthetic pathways. A highly efficient synthesis of [1-¹³C, ¹⁸O]- and [1-¹³C, ²H₂]-glycerol is described in which the ¹³C label is introduced using cyanide. The ¹⁸O label was introduced by a Pinner synthesis and reduction of the ester 5 allowed incorporation of the ²H labels.     

Overexpression of glucose-6-phosphate dehydrogenase in genetically modified Saccharomyces cerevisiae

Glucose-6-phosphate dehydrogenase (G6PD) (EC 1.1.1.49) is an abun dant enzyme in Saccharomyces cerevisiae. This enzyme is of great interest as an analytical reagent because it is used in a large number of quantitative assays. A strain of S. cerevisiae was genetically modified to improve G6PD production during aerobic culture. The modifications are based on cloning the G6PD sequence under the control of promoters that are upregulated by the carbon source used for yeast growth. The results showed that S. cerevisiae acquired from a commercial source and the same strain produced by aerobic cultivation under controlled conditions provided very similar G6PD. However, G6PD production by genetically modified S. cerevisiae produced very high enzyme activity and showed to be the most effective procedure to obtain glucose-6-phosphate dehydrogenase. As a consequence, the cost of producing G6PD can be significantly reduced by using strains that contain levels of G6PD up to 14-fold higher than the level of G6PD found in commercially available strains.     

Radiation-induced radicals in glucose-1-phosphate. II. DFT analysis of structures and possible formation mechanisms

Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1-R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.     

Estimation of the biological variation of glucose-6-phosphate dehydrogenase in dried blood spots

Models based on biological variation provide a well-accepted database with reliable information for clinical laboratories for all purposes including screening, diagnosis and follow-up. Newborn screening laboratories use a blood spotted paper matrix to measure the analytes. This matrix medium is certainly different than body fluid matrix medium. After long-term monitoring of the performance of the Glucose-6-Phosphate Dehydrogenase Kit (R&D Diagnostics OSMMR 2000-D G6PD), the results obtained from the variation analysis were statistically evaluated. Analytical coefficient of variation, CV _A, was found to be 5.41%. The CV _A derived from between run assays was 5.32%, while within-subject biological coefficient of variation, CV _I, was 7.26%. Since minimum performance is defined as CV _A< 0.750 CV _I , CV _A should be lower than 5.44%. The analytical bias in calculation of total error was chosen to evaluate the performance of this assay. In this aspect, CV _G, between-subject biological coefficient of variation, was found to be equal to 10.35%. B _A was found to be 4.12%, which is lower than 4.74%, which means that it is acceptable. Therefore, the minimum quality specification for total error allowable is . When the relevant results obtained in this study were substituted in this formula, TE _a was found to be 13.7% for G6PD measurement in dried blood spots on paper filter matrix. It is expected that this figure will be helpful for the performance evaluation of newborn screening laboratories performing G6PD screening. We have been using error grid graphs for the evaluation of our external quality assurance survey results for the last two years, only because there was no data for assays employing filter matrix. Even the TE _a already reported for EDTA whole blood samples used in G6PD assays has been remarkably high, which can easily create the wrong impression that G6PD is not a reliable test to perform from blood spot cards. The present study shows that this assay is adequately reliable even when performed from dried blood spot matrix. However, we believe that the combination of total allowable error, error grid graphs with a well-defined cut off is the best approach to obtain an accurate performance evaluation for this test.Presented at the 10th Conference Quality in the Spotlight, March 2005, Antwerp, Belgium.     

The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate

The glmS ribozyme riboswitch is the first known natural catalytic RNA that employs a small-molecule cofactor. Binding of glucosamine-6-phosphate (GlcN6P) uncovers the latent self-cleavage activity of the RNA, which adopts a catalytically competent conformation that is nonetheless inactive in the absence of GlcN6P. Structural and analogue studies suggest that the amine of GlcN6P functions as a general acid-base catalyst, while its phosphate is important for binding affinity. However, the solution pK(a) of the amine is 8.06 ± 0.05, which is not optimal for proton transfer. Here we used Raman crystallography directly to determine the pK(a)'s of GlcN6P bound to the glmS ribozyme. Binding to the RNA lowers the pK(a) of the amine of GlcN6P to 7.26 ± 0.09 and raises the pK(a) of its phosphate to 6.35 ± 0.09. Remarkably, the pK(a)'s of these two functional groups are unchanged from their values for free GlcN6P (8.06 ± 0.05 and 5.98 ± 0.05, respectively) when GlcN6P binds to the catalytically inactive but structurally unperturbed G40A mutant of the ribozyme, thus implicating the ribozyme active site guanine in pK(a) tuning. This is the first demonstration that a ribozyme can tune the pK(a) of a small-molecule ligand. Moreover, the anionic glmS ribozyme in effect stabilizes the neutral amine of GlcN6P by lowering its pK(a). This is unprecedented and illustrates the chemical sophistication of ribozyme active sites.     

Biomimetic total syntheses of linderaspirone A and bi-linderone and revisions of their biosynthetic pathways

Simple exposure to sunlight is sufficient for triggering photochemical [2 + 2] cycloaddition-Cope or radical rearrangement cascades in the naturally occurring methyl linderone, leading to efficient biomimetic total syntheses of linderaspirone A and bi-linderone, two recently discovered bioactive spirocyclopentenedione natural products.     

Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways

Lanthipeptides are characterized by thioether crosslinks formed by post-translational modifications. The cyclization process that favors a single ring pattern over many other possible ring patterns has been the topic of much speculation. Recent studies suggest that for some systems the cyclization pattern and stereochemistry is determined not by the enzyme, but by the sequence of the precursor peptide. However, the factors that govern the outcome of the cyclization process are not understood. This study presents the three-dimensional structures of seven lanthipeptides determined by nuclear magnetic resonance spectroscopy, including five prochlorosins and the two peptides that make up cytolysin, a virulence factor produced by Enterococcus faecalis that is directly linked to human disease. These peptides were chosen because their substrate sequence determines either the ring pattern (prochlorosins) or the stereochemistry of cyclization (cytolysins). We present the structures of prochlorosins 1.1, 2.1, 2.8, 2.10 and 2.11, the first three-dimensional structures of prochlorosins. Our findings provide insights into the molecular determinants of cyclization as well as why some prochlorosins may be better starting points for library generation than others. The structures of the large and small subunits of the enterococcal cytolysin show that these peptides have long helical stretches, a rare observation for lanthipeptides characterized to date. These helices may explain their pore forming activity and suggest that the small subunit may recognize a molecular target followed by recruitment of the large subunit to span the membrane.

To understand factors that determine ring pattern and stereochemistry of thioether cyclization of lanthipeptide natural products, the structures of five prochlorosins (blue) and two enterococcal cytolysins (red) were determined by NMR spectroscopy.     

A new family of Ru complexes for water oxidation

Reaction of the bridging ligand 3,6-bis-[6'-(1' ',8' '-naphthyrid-2' '-yl)-pyrid-2'-yl]pyridazine (1) with [Ru(DMSO)4Cl2] in aqueous ethanol followed by excess 4-substituted pyridine (4-R-py) in the presence of triethylamine provides a series of three well-organized dinuclear complexes characterized by 1H NMR, MS, and X-ray. Mononuclear analogues are prepared from 4-tert-butyl-2,6-di(1',8'-naphthyrid-2'-yl)pyridine (5) and characterized in a similar fashion. All six complexes show electronic absorption and redox properties consistent with the electron donor/acceptor ability of the axial 4-R-py ligand. When an acetonitrile solution of the catalyst is added to an aqueous Ce(IV)-CF3SO3H solution (pH = 1.0) at 24 degrees C, oxygen evolution is observed for both mono and dinuclear systems. Turnover numbers range from 50 to 3200 with the best results being found when the axial ligand is 4-methylpyridine (mononuclear TN = 580 and dinuclear TN = 3200).