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Magic Spot Nucleotides (MSN) regulate the stringent response, a highly conserved bacterial stress adaptation mechanism, enabling survival under adverse external challenges. In times of antibiotic crisis, a detailed understanding of stringent response is essential, as potentially new targets for pharmacological intervention could be identified. In this study, we delineate the MSN interactome in Escherichia coli and Salmonella typhimurium applying a family of trifunctional photoaffinity capture compounds. We introduce MSN probes covering a diverse phosphorylation pattern, such as pppGpp, ppGpp, and pGpp. Our chemical proteomics approach provides datasets of putative MSN receptors both from cytosolic and membrane fractions that unveil new MSN targets. We find that the activity of the non-Nudix hydrolase ApaH is potently inhibited by pppGpp, which itself is converted to pGpp by ApaH. The capture compounds described herein will be useful to identify MSN interactomes across bacterial species.

RATIONALE A rapid and precise analytical method for the investigation of natural products is required for pathway monitoring of the biosynthesis of secondary metabolites. Phenalinolactones, used in antibiotic research, are produced by Streptomyces sp. Tu6071. For the analysis of those compounds, prior to mass spectrometric analysis, an efficient separation technique is required. METHODS For the identification of phenalinolactones from liquid cultures of Streptomyces sp. Tu6071, a new method comprising the combination of solid-phase extraction (SPE) prior to liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) was established. MS/MS product ion scans were applied for phenalinolactone detection and structure elucidation, performed in negative mode and optimized for sensitivity and specificity. For the discovery of new intermediates, a MS/MS precursor ion scan was applied. RESULTS Analysis of the extracts revealed that the Oasis® MAX cartridge, containing a quaternary amine functionality, is the most efficient SPE material for purification of phenalinolactones, since it allowed sufficient enrichment and detection of intermediates from the biosynthetic pathway by LC/ESI-MS/MS. Using the precursor ion scan technique, two new secondary metabolites, PL IM1 with m/z 672.6 and PL IM2 with m/z 433.3, have been detected. The structures of the new intermediates are postulated and arranged into the biosynthetic pathway of phenalinolactones. CONCLUSIONS A precise analytical method was established for the identification of phenalinolactones by combining purification from Streptomyces using SPE prior to LC/ESI-MS/MS. By optimising LC/ESI-MS/MS settings, this method has been successfully applied for pathway monitoring of secondary metabolites. Application of a precursor ion scan allowed for the identification of unknown intermediates in biosynthetic pathways. Copyright © 2014 John Wiley & Sons, Ltd.

The development of reliable analytic methods, capable of separating mixtures of secondary metabolites as well as providing structural information, is essential for the investigation of secondary metabolites, e.g. from Streptomyces. Here we report a liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method using a triple quadrupole mass analyzer for the structural elucidation of caprazamycins and liposidomycins from culture extracts of the wild-type producer strains. Comparison of the fragmentation patterns in positive as well as in negative ionization mode revealed several characteristic product ions used for identification of six new caprazamycins. Furthermore, a chromatographic method for the purification of nucleosides from cell cultures using a boronic acid gel was adapted for the partial purification of the culture extracts. Copyright © 2011 John Wiley & Sons, Ltd.

The depsipeptide antibiotic hormaomycin, which is produced by Streptomyces griseoflavus W-384, contains a 5-chloropyrrole moiety. In the producer strain we identified the gene hrmQ that shows sequence similarity to FADH(2)-dependent halogenases. This gene was cloned and heterologously expressed in Streptomyces roseochromogenes var. oscitans DS12.976, which is the producer of the aminocoumarin antibiotic clorobiocin, which contains a 5-methylpyrrole moiety. For the present experiment, we used a mutant of this strain in which the respective pyrrole-5-methyltransferase had been inactivated. Expression of the halogenase hrmQ in this mutant strain led to the formation of two new clorobiocin derivatives that carried a 5-chloropyrrole moiety. These compounds were isolated on a preparative scale, their structures were elucidated by (1)H NMR spectroscopy and mass spectrometry, and their antibacterial activity was determined. The substrate of HrmQ is likely to be a pyrrole-2-carboxyl-S-[acyl carrier protein] thioester. If this assumption is true, this study presents the first experiment in combinatorial biosynthesis that uses a halogenase that acts on an acyl carrier protein-bound substrate.

Many secondary metabolites of clinical importance have been isolated from different Streptomyces species. As most of the natural producers remain difficult to handle genetically, heterologous expression of an entire biosynthetic gene cluster in a well characterised host allows improved possibilities for modifications of the desired compound by manipulation of the biosynthetic genes. However, the large size of a functional gene cluster often prevents its direct cloning into a single cosmid clone. Here we describe a successful strategy to assemble the entire coumermycin A1 biosynthetic gene cluster (38.6 kb) into a single cosmid clone by lambda RED recombination technology. Heterologous expression of the reconstituted gene cluster in Streptomyces coelicolor M512 resulted in the heterologous production of coumermycin A1. Inactivation of the methyltransferase gene couO--responsible for the C-methylation at the 8-positions of the aminocoumarin moieties in coumermycin A1--and heterologous expression of the modified cluster resulted in an accumulation of a C-8-unsubstituted coumermycin A1 derivative. Subsequent expression of the halogenase gene clo-hal from the clorobiocin gene cluster in the heterologous producer strain led to the formation of two new hybrid antibiotics, containing either one or two chlorine atoms. The identities of the new compounds were verified by LC-MS, and their antibacterial activities were tested against Bacillus subtilis in an agar diffusion assay.

The zinc dehydrophthalocyanine 2 and zinc dehydrobenzoporhyrazine 8 a were generated from the 1N-aminobenzotriazole-annulated zinc phtalocyanine 1 and zinc benzoporhyrazine 8, respectively, by oxidation with Pb(OAc)(4) in different solvents, for example, diethyl ether, tetrahydrofuran, acetic acid, and benzene. The reactivity of 2 and 8 a was studied in detail. These species not only easily undergo Diels-Alder additions with dienes, but also the used solvents can be added. Among the addition products with solvents ethoxy-, acetoxy-, acetoxybutyloxy-substituted and barrelen-fused phthalocyanines and benzoporpyrazines were isolated. No products resulting from the dimerization of two dehydro species were observed either for 2 or 8 a. Analysis of the reaction products in comparison with those obtained by oxidation of 1-aminobenzotriazole 15 under similar conditions proves a higher reactivity (electrophilicity) of the dehydro-PcZn 2 and dehydro-PzZn 8 a in comparison with unsubstituted benzyne towards the solvents used, such as diethyl ether and benzene.

The synthesis of 5,6-dicyano-1H-1,2,3-benzotriazole (2) was significantly simplified and its overall yield was increased. This opens up the possibility for an extended use of 2 as a precursor for triazole-functionalized phthalocyanines. One of them, the unsymmetrical {9,10,16,17,23,24-hexakis(3,5-di-tert-butylphenoxy)[1,2,3]triazolo[4,5-b]phthalocyaninato}-zinc (5) was prepared in a statistical condensation of 2 and 4,5-bis(3,5-di-tert-butylphenoxy)phthalonitrile (3) with subsequent separation by column chromatography. The triazole-functionalized (phthalocyanine)zinc complex 5 shows interesting spectral properties in solutions depending on the chemical medium because of the reactions which are typical for the triazole fragment. These are acid ionization of NH, coordination to metal ions, N-alkylation and N-acylation, among others. Compound 5 was characterized in detail using UV/Vis, 1H and 13C NMR spectroscopy, mass spectrometry (MALDI-TOF), and elemental analysis. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

The reactivity of the 2,3-dibromobenzo-annulated 2,3,7,8,12,13-hexakis(m-trifluoromethylphenyl)porphyrazine magnesium complex 1 towards butyllithium and tert-butylmagnesium chloride in the presence of metallic magnesium was studied. It was found that n-butyllithium reacts mainly with the porphyrazine macrocycle to give tetraazachlorins and other reduction products, similarly to porphyrins. On treatment of 1 with tBuMgCl and Mg, dehydroporphyrazine 4 (arynoporphyrazine) was generated and trapped with furan, confirming the possibility of the formation of a dehydrophthalocyanine. The structures of the products were verified by UV/Vis and NMR spectroscopy, and also mass spectrometry (MALDI-TOF). Utilization of the tetrapyrrolic macrocycle 1 for this type of reaction may become a new synthetic strategy for unsymmetrical peripheral derivatization of phthalocyanines and related compounds. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Three new aminocoumarin antibiotics, termed ferulobiocin, 3-chlorocoumarobiocin and 8'-dechloro-3-chlorocoumarobiocin, were isolated from the culture broth of a Streptomyces coelicolor M512 strain expressing a modified clorobiocin biosynthetic gene cluster. Structural analysis showed that these new aminocoumarins were very similar to clorobiocin, with a substituted 4-hydroxycinnamoyl moieties instead of the prenylated 4-hydroxybenzoyl moiety of clorobiocin. The possible biosynthetic origin of these moieties is discussed.