Peptide natural products exhibit broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce Natural Product Peptidogenomics (NPP), a new mass spectrometry-guided genome mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo MSn structures to genomics-based structures following current biosynthetic logic. In this study we demonstrate that NPP enabled the rapid characterization of >10 chemically diverse ribosomal and nonribosomal peptide natural products of novel composition from streptomycete bacteria as a proof of concept to begin automating the genome mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which from well-characterized model streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms.

The antineoplastic agent didemnin B from the Caribbean tunicate Trididemnum solidum was the first marine drug to be clinically tested in humans. Because of its limited supply and its complex cyclic depsipeptide structure, considerable challenges were encountered during didemnin B's development that continue to limit aplidine (dehydrodidemnin B), which is currently being evaluated in numerous clinical trials. Herein we show that the didemnins are bacterial products produced by the marine α-proteobacteria Tistrella mobilis and Tistrella bauzanensis via a unique post-assembly line maturation process. Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain KA081020-065 with its five circular replicons revealed the putative didemnin biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did locus encodes a 13-module hybrid nonribosomal peptide synthetase-polyketide synthase enzyme complex organized in a co-linear arrangement for the synthesis of the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial colonies captured the time-dependent extracellular conversion of the didemnin X and Y precursors to didemnin B in support of an unusual post-synthetase activation mechanism. Significantly, the discovery of the didemnin biosynthetic gene cluster may provide a long-term solution to the supply problem that presently hinders this group of marine natural products and pave the way for the genetic engineering of new didemnin congeners.

Jasmonic acid (JA) plays pivotal roles in diverse plant biological processes, including wound response. Chloroplast lipid hydrolysis is a critical step for JA biosynthesis, but the mechanism of this process remains elusive. We report here that DONGLE (DGL), a homolog of DEFECTIVE IN ANTHER DEHISCENCE1 (DAD1), encodes a chloroplast-targeted lipase with strong galactolipase and weak phospholipase A(1) activity. DGL is expressed in the leaves and has a specific role in maintaining basal JA content under normal conditions, and this expression regulates vegetative growth and is required for a rapid JA burst after wounding. During wounding, DGL and DAD1 have partially redundant functions for JA production, but they show different induction kinetics, indicating temporally separated roles: DGL plays a role in the early phase of JA production, and DAD1 plays a role in the late phase of JA production. Whereas DGL and DAD1 are necessary and sufficient for JA production, phospholipase D appears to modulate wound response by stimulating DGL and DAD1 expression.

Meroterpenoids are mixed polyketide-terpenoid natural products with a broad range of biological activities. Herein, we present the structures of four new meroterpenoid antibiotics, merochlorins A–D, produced by the marine bacterium Streptomyces sp. strain CNH-189, which possess novel chemical skeletons unrelated to known bacterial agents. Draft genome sequencing, mutagenesis and heterologous biosynthesis in the genome-minimized model actinomycete Streptomyces coelicolor provided a 57.6 kb gene cluster that contains two genes encoding rare bacterial vanadium-dependent haloperoxidase (VHPO) genes. Pathway expression of two different fosmid clones that differ largely by the presence or absence of the VHPO gene mcl40, resulted in the differential biosynthesis of merochlorin C, suggesting that Mcl40 catalyzes an unprecedented 15-membered chloronium-induced macrocyclization reaction converting merochlorin D to merochlorin C.

Bacteria within the skin microbiome of some individuals produce an antimetabolite that inhibits tumor growth.

Six new (1, 2, and 5-8) and three known (3, 4, and 9) butenolide metabolites were isolated from the tunicate Pseudodistoma antinboja by activity-guided fractionations. The structures were elucidated by combined NMR and MS spectroscopic methods. These compounds were evaluated for their antibacterial activity, and most of them exhibited moderate to significant activity that selectively targeted Gram-positive strains and did not exhibit cytotoxicity in the MTT assay at 100 μM. Cadiolides 5-9 in particular exhibited significant antibacterial activity that was comparable to or even better than those of marketed drugs such as vancomycin and linezolid against all of the drug-resistant strains tested.

Monitoring fluctuations in enzyme overexpression facilitates early tumor detection and excision. An AIEgen probe (DQM‐ALP) for the imaging of alkaline phosphatase (ALP) activity was synthesized. The probe consists of a quinoline‐malononitrile (QM) core decorated with hydrophilic phosphate groups as ALP‐recognition units. The rapid liberation of DQM‐OH aggregates in the presence of ALP resulted in aggregation‐induced fluorescence. The up‐regulation of ALP expression in tumor cells was imaged using DQM‐ALP. The probe permeated into 3D cervical and liver tumor spheroids for imaging spatially heterogeneous ALP activity with high spatial resolution on a two‐photon microscopy platform, providing the fluorescence‐guided recognition of sub‐millimeter tumorigenesis. DQM‐ALP enabled differentiation between tumor and normal tissue ex vivo and in vivo, suggesting that the probe may serve as a powerful tool to assist surgeons during tumor resection.

Fijiolide A, a potent inhibitor of TNF-α induced NFκB activation, along with fijiolide B, were isolated from a marine-derived bacterium of the genus Nocardiopsis. The planar structures of fijiolides A (1) and B (2) were elucidated by interpretation of 2D NMR spectroscopic data, while the absolute configurations of these compounds were defined by interpretation of circular dichroism (CD) and 2D NMR data combined with application of the advanced Mosher's method. Fijiolides A and B are related to several recently isolated chloroaromatic compounds, which appear to be the Bergman cyclization products of enediyne precursors. Fijiolide A reduced TNF-α induced NFκB activation by 70.3%, with an IC 50 value of 0.57 µM. Fijiolide B demonstrated less inhibition, only 46.5%, without dose-dependence. The same pattern was also observed with quinone reductase (QR) activity: fijiolide A was found to induce quinone reductase-1 (QR1), with an induction ratio (IR) of 3.5 at a concentration of 20 µg/mL (28.4 µM). The concentration required to double activity (CD) was 1.8 µM. Fijiolide B did not affect QR1 activity, indicating the importance of the nitrogen substitution pattern for biological activity. Based on these data, fijiolide A is viewed as a promising lead for more advanced anticancer testing.Nature is an important resource for the discovery of anticancer drugs. The relevance of the marine environment as a source of novel anticancer compounds has been validated by discovery ca. 2,500 new metabolites with antiproliferative activity.1 Bacteria belonging to the order Actinomycetales, commonly known as actinomycetes, have provided nearly 50% of the bioactive microbial natural products discovered as of 2002.2 Although most microbial small molecule discovery efforts have focused on actinomycetes from terrestrial environments, marine-derived actinomycetes are proving to be an important resource that has led to the discovery of biologically active molecules with unique chemical structures.3 Excellent examples are the salinosporamides4a and marinomycins.4b Salinosporamide A, isolated from Salinispora tropica, is a potent 20S proteasome inhibitor that recently completed phase I clinical trials for treatment of solid tumors, lymphomas, and multiple myeloma. The marinomycins isolated from a "Marinispora" sp. showed significant antimicrobial activity against drug-resistant bacterial pathogens and selective cancer cell cytotoxicity against melanoma cell lines.4bCorresponding Author: Tel: 1-858-534-2133; Fax: 1-858-534-1318; wfenical@ucsd.edu. Supporting Information Available: The 1 H, 13 C, and 2D NMR spectra of fijiolide A (1) and 1 H spectrum of fijiolide B (2), and 1 H NMR spectrum of MTPA esters 3a, 3b, 4a, 4b, 6a, 6b, and 1 H NMR spectrum of acetonide 5 are available free of charge via the Internet at http://pubs.acs.org. As part of a program to explore marine bacterial metabolites as inhibitors of tumor initiation and promotion, we have targeted nuclear factor kappa B (NFκB), a transcription factor that regulates the expressi...