Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.

Novel antibiotics are urgently needed to address the looming global crisis of antibiotic resistance. Historically, the primary source of clinically used antibiotics has been microbial secondary metabolism. Microbial genome sequencing has revealed a plethora of uncharacterized natural antibiotics that remain to be discovered. However, the isolation of these molecules is hindered by the challenge of linking sequence information to the chemical structures of the encoded molecules. Here, we present PRISM 4, a comprehensive platform for prediction of the chemical structures of genomically encoded antibiotics, including all classes of bacterial antibiotics currently in clinical use. The accuracy of chemical structure prediction enables the development of machine-learning methods to predict the likely biological activity of encoded molecules. We apply PRISM 4 to chart secondary metabolite biosynthesis in a collection of over 10,000 bacterial genomes from both cultured isolates and metagenomic datasets, revealing thousands of encoded antibiotics. PRISM 4 is freely available as an interactive web application at http://prism.adapsyn.com .

Ecological Roles of Tryptanthrin, Indirubin and N-Formylanthranilic Acid in Isatis indigotica: Phytoalexins or Phytoanticipins?

Leaves of the plant species Isatis indigotica Fortune ex Lindl. (Chinese woad) produce the metabolites tryptanthrin, indirubin and N-formylanthranilic acid upon spraying with an aqueous solution of copper chloride but not after spraying with water. The antifungal activities of these metabolites against the phytopathogens Alternaria brassicicola, Leptosphaeria maculans and Sclerotinia sclerotiorum established that tryptanthrin is a much stronger growth inhibitor of L. maculans than the phytoalexin camalexin. The biosynthetic precursors of tryptanthrin and N-formylanthranilic acid are proposed based on the deuterium incorporations of isotopically labeled compounds. The overall results suggest that tryptanthrin is a phytoalexin and indirubin and N-formylanthranilic acid are phytoanticipins in the plant species I. indigotica and that chemical diversity and biodiversity are intimately connected.

Interrogation of biosynthetic pathways of the cruciferous phytoalexins nasturlexins with isotopically labelled compounds.

The discovery of the first non-indolyl cruciferous phytoalexins nasturlexins A and B together with cyclonasturlexin and brassinin, all chemical defenses of watercress plants (Nasturtium officinale R. Br.), revealed the co-occurrence of two parallel defense pathways, the tryptophan (Trp) pathway and the phenylalanine (Phe) pathway in crucifers. Similar to watercress, winter cress (Barbarea vulgaris R. Br.) and upland cress [B. verna (P. Mill.) Aschers] produce Phe derived phytoalexins, the nasturlexins C and D together with their counterpart sulfoxides. A detailed chemical understanding of the biosynthetic pathways of these phytoalexins facilitates their metabolic engineering. To this end, the biosynthetic pathways of cyclonasturlexin, nasturlexins A-D and corresponding sulfoxides in cress plants were investigated using isotopically labelled compounds. Except for the carbon atom of the thiomethyl groups of nasturlexins, the origin of all carbon atoms and nitrogen of nasturlexins was established to be homophenylalanine. A detailed map of the biosynthetic intermediates between phenylethyl isothiocyanates and nasturlexins A-D and sulfoxides in upland cress, winter cress and watercress is proposed. An application beyond these findings could lead to "designer crops" containing a wider range of chemical defenses that could make such crops more resistant to pests and diseases, a greatly advantageous trait.

Synthesis of stable isotope-labeled nasturlexins and potential precursors to probe biosynthetic pathways of cruciferous phytoalexins.

The syntheses of perdeuterated phytoalexins nasturlexins A and C, and putative biosynthetic precursors, including phenylethyl isothiocyanates and phenylethyl dithiocarbamates, using commercially available [2,3,4,5,6-D5 ]phenylalanine, [2,3,4,5,6-D5 ]nitrobenzene, and [2,3,4,5,6-D5 ]benzaldehyde are described. In addition, application of an efficient deuterium-hydrogen exchange transformation to nonlabeled starting materials allowed access to new deuterated compounds, including 3-hydroxyphenylethyl glucosinolate.

Defense and signalling metabolites of the crucifer Erucastrum canariense: Synchronized abiotic induction of phytoalexins and galacto-oxylipins.

Erucastrum canariense Webb & Berthel. (Brassicaceae) is a wild crucifer that grows in rocky soils, in salt and water stressed habitats, namely in the Canary Islands and similar environments. Abiotic stress induced by copper chloride triggered formation of a phytoalexin and galacto-oxylipins in E. canariense, whereas wounding induced galacto-oxylipins but not phytoalexins. Analysis of the metabolite profiles of leaves of E. canariense followed by isolation and structure determination afforded the phytoalexin erucalexin, the phytoanticipin indolyl-3-acetonitrile, the galacto-oxylipins arabidopsides A, C, and D, and the oxylipin 12-oxophytodienoic acid. In addition, arabidopsides A and D were also identified in extracts of leaves of Nasturtium officinale R. Br.

Expanding the nasturlexin family: Nasturlexins C and D and their sulfoxides are phytoalexins of the crucifers Barbarea vulgaris and B. verna.

The metabolites produced in leaves of the crucifers winter cress (Barbarea vulgaris) and upland cress (Barbarea verna) abiotically elicited were investigated and their chemical structures were elucidated by analyses of spectroscopic data and confirmed by syntheses. Nasturlexins C and D and their sulfoxides are cruciferous phytoalexins displaying antifungal activity against the crucifer pathogens Alternaria brassicicola, Leptosphaeria maculans and Sclerotinia sclerotiorum. The biosynthesis of these metabolites is proposed based on pathways of cruciferous indolyl phytoalexins. This work indicates that B. vulgaris and B. verna have great potential as sources of defense pathways transferable to agriculturally important crops within the Brassica species.

Non-indolyl cruciferous phytoalexins: Nasturlexins and tridentatols, a striking convergent evolution of defenses in terrestrial plants and marine animals?

Highly specialized chemical defense pathways are a particularly noteworthy metabolic characteristic of sessile organisms, whether terrestrial or marine, providing protection against pests and diseases. For this reason, knowledge of the metabolites involved in these processes is crucial to producing ecologically fit crops. Toward this end, the elicited chemical defenses of the crucifer watercress (Nasturtium officinale R. Br.), i.e. phytoalexins, were investigated and are reported. Almost three decades after publication of cruciferous phytoalexins derived from (S)-Trp, phytoalexins derived from other aromatic amino acids were isolated; their chemical structures were determined by analyses of their spectroscopic data and confirmed by synthesis. Nasturlexin A, nasturlexin B, and tridentatol C are hitherto unknown phenyl containing cruciferous phytoalexins produced by watercress under abiotic stress; tridentatol C is also produced by a marine animal (Tridentata marginata), where it functions in chemical defense against predators. The biosynthesis of these metabolites in both a terrestrial plant and a marine animal suggests a convergent evolution of unique metabolic pathways recruited for defense.