An unusual flavin-dependent halogenase from the metagenome of the marine sponge Theonella swinhoei WA

The authors thank EU BlueGenics (Seventh Framework Programme, Collaborative project “BlueGenics”, Grant no. 311848 RJMG and JP), the SNF (Grant no.205321_165695 to JP), the Helmut Horten Foundation (JP), and ERAIB (Grant no. 031A338A KHVP and RJMG) for funding.Uncultured bacteria from sponges have been demonstrated to be responsible for the generation of many potent, bioactive natural products including halogenated metabolites.1 The identification of gene clusters from the metagenomes of such bacterial communities enables the discovery of enzymes that mediate new and useful chemistries and allows insight to be gained into the biogenesis of potentially pharmacologically important natural products. Here we report a new pathway to the keramamides (krm); the first functional evidence for the existence of a distinct producer in the Theonella swinhoei WA chemotype is revealed, and a key enzyme on the pathway, a unique flavin dependent halogenase with a broad substrate specificity, and with potential as a useful new biocatalytic tool is described.PostprintPeer reviewe

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

3‐Hydroxypropionate production from myo ‐inositol by the gut acetogen Blautia schinkii

Abstract Species of the genus Blautia are not only abundant in the human gut but also contribute to human well‐being. Our study demonstrates that the gut acetogen Blautia schinkii can grow on myo ‐inositol. We identified the pathway of myo ‐inositol degradation through a combination of physiological and biochemical studies, genome‐wide expression profiling and homology searches. Initially, myo ‐inositol is oxidized to 2‐keto‐ myo ‐inositol. This compound is then metabolized by a series of enzymes – a dehydratase, hydrolase, isomerase and kinase – to form 2‐deoxy‐5‐keto‐ d ‐gluconic acid 6‐phosphate. This intermediate is split by an aldolase into malonate semialdehyde and dihydroxyacetone phosphate, which is an intermediate of the Embden–Meyerhof–Parnas pathway. This pathway leads to the production of pyruvate and, subsequently, acetate. Concurrently, malonate semialdehyde is reduced to 3‐hydroxypropionate (3‐HP). The genes responsible for myo ‐inositol degradation are clustered on the genome, except for the gene encoding the aldolase. We identified the putative aldolase Fba_3 and 3‐HP dehydrogenase Adh1 encoding genes bioinformatically and verified them biochemically using enzyme assays with heterologously produced and purified protein. The major fermentation end products were 3‐HP and acetate, produced in similar amounts. The production of the unusual fermentation end product 3‐HP is significant not only for human health but also for the potential bioindustrial production of this highly desired compound

An unusual flavin-dependent halogenase from the metagenome of the marine sponge <i>Theonella swinhoei</i> WA

Uncultured bacteria from sponges have been demonstrated to be responsible for the generation of many potent, bioactive natural products including halogenated metabolites.1 The identification of gene clusters from the metagenomes of such bacterial communities enables the discovery of enzymes that mediate new and useful chemistries and allows insight to be gained into the biogenesis of potentially pharmacologically important natural products. Here we report a new pathway to the keramamides (krm); the first functional evidence for the existence of a distinct producer in the Theonella swinhoei WA chemotype is revealed, and a key enzyme on the pathway, a unique flavin dependent halogenase with a broad substrate specificity, and with potential as a useful new biocatalytic tool is described

A Multi-Producer Microbiome Creates Chemical Diversity in the Marine Sponge Mycale hentscheli

Rust M, Helfrich EJN, Freeman MF, et al. A Multi-Producer Microbiome Creates Chemical Diversity in the Marine Sponge Mycale hentscheli. In: MARINE DRUGS. Vol 18. Basel: Mdpi; 2020

A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli.

Rust M, Helfrich EJN, Freeman MF, et al. A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(17):9508-9518.Bacterial specialized metabolites are increasingly recognized as important factors in animal-microbiome interactions: for example, by providing the host with chemical defenses. Even in chemically rich animals, such compounds have been found to originate from individual members of more diverse microbiomes. Here, we identified a remarkable case of a moderately complex microbiome in the sponge host Mycale hentscheli in which multiple symbionts jointly generate chemical diversity. In addition to bacterial pathways for three distinct polyketide families comprising microtubule-inhibiting peloruside drug candidates, mycalamide-type contact poisons, and the eukaryotic translation-inhibiting pateamines, we identified extensive biosynthetic potential distributed among a broad phylogenetic range of bacteria. Biochemical data on one of the orphan pathways suggest a previously unknown member of the rare polytheonamide-type cytotoxin family as its product. Other than supporting a scenario of cooperative symbiosis based on bacterial metabolites, the data provide a rationale for the chemical variability of M. hentscheli and could pave the way toward biotechnological peloruside production. Most bacterial lineages in the compositionally unusual sponge microbiome were not known to synthesize bioactive metabolites, supporting the concept that microbial dark matter harbors diverse producer taxa with as yet unrecognized drug discovery potential. Copyright © 2020 the Author(s). Published by PNAS

Bacillimidazoles A&minus;F, Imidazolium-Containing Compounds Isolated from a Marine Bacillus

Chemical investigations of a marine sponge-associated Bacillus revealed six new imidazolium-containing compounds, bacillimidazoles A&ndash;F (1&ndash;6). Previous reports of related imidazolium-containing natural products are rare. Initially unveiled by timsTOF (trapped ion mobility spectrometry) MS data, extensive HRMS and 1D and 2D NMR analyses enabled the structural elucidation of 1&ndash;6. In addition, a plausible biosynthetic pathway to bacillimidazoles is proposed based on isotopic labeling experiments and invokes the highly reactive glycolytic adduct 2,3-butanedione. Combined, the results of structure elucidation efforts, isotopic labeling studies and bioinformatics suggest that 1&ndash;6 result from a fascinating intersection of primary and secondary metabolic pathways in Bacillus sp. WMMC1349. Antimicrobial assays revealed that, of 1&ndash;6, only compound six displayed discernible antibacterial activity, despite the close structural similarities shared by all six natural products