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1. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

   https://doi.org/10.1073/pnas.2311245121  

   Bradshaw, Alexander J; Ramírez-Cruz, Virginia; Awan, Ali R; Furci, Giuliana; Guzmán-Dávalos, Laura; Dentinger, Bryn_T M (January 2024, Proceedings of the National Academy of Sciences)

   Psychoactive mushrooms in the genusPsilocybehave immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species ofPsilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny ofPsilocybeusing shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage ofPsilocybearose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose inPsilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster withinPsilocybe. 

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2. Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α‐Diazoester Production

   https://doi.org/10.1002/anie.202304646  

   Van Cura, Devon; Ng, Tai L.; Huang, Jing; Hager, Harry; Hartwig, John F.; Keasling, Jay D.; Balskus, Emily P. (May 2023, Angewandte Chemie International Edition)

   Abstract Azaserine is a bacterial metabolite containing a biologically unusual and synthetically enabling α‐diazoester functional group. Herein, we report the discovery of the azaserine (aza) biosynthetic gene cluster fromGlycomyces harbinensis. Discovery of related gene clusters reveals previously unappreciated azaserine producers, and heterologous expression of theazagene cluster confirms its role in azaserine assembly. Notably, this gene cluster encodes homologues of hydrazonoacetic acid (HYAA)‐producing enzymes, implicating HYAA in α‐diazoester biosynthesis. Isotope feeding and biochemical experiments support this hypothesis. These discoveries indicate that a 2‐electron oxidation of a hydrazonoacetyl intermediate is required for α‐diazoester formation, constituting a distinct logic for diazo biosynthesis. Uncovering this biological route for α‐diazoester synthesis now enables the production of a highly versatile carbene precursor in cells, facilitating approaches for engineering complete carbene‐mediated biosynthetic transformations in vivo. 

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3. Discovery and Biosynthesis of a Structurally Dynamic Antibacterial Diterpenoid

   https://doi.org/10.1002/anie.202102453  

   Zhu, Chenxi; Xu, Baofu; Adpressa, Donovon A.; Rudolf, Jeffrey D.; Loesgen, Sandra (May 2021, Angewandte Chemie International Edition)

   Abstract A new bicyclic diterpenoid, benditerpenoic acid, was isolated from soil‐dwellingStreptomycessp. (CL12‐4). We sequenced the bacterial genome, identified the responsible biosynthetic gene cluster, verified the function of the terpene synthase, and heterologously produced the core diterpene. Comparative bioinformatics indicated thisStreptomycesstrain is phylogenetically unique and possesses nine terpene synthases. The absolute configurations of the newtrans‐fused bicyclo[8.4.0]tetradecanes were achieved by extensive spectroscopic analyses, including Mosher's analysis,J‐based coupling analysis, and computations based on sparse NMR‐derived experimental restraints. Interestingly, benditerpenoic acid exists in two distinct ring‐flipped bicyclic conformations with a rotational barrier of ≈16 kcal mol⁻¹in solution. The diterpenes exhibit moderate antibacterial activity against Gram‐positive bacteria including methicillin and multi‐drug resistantStaphylococcus aureus. This is a rare example of an eunicellane‐type diterpenoid from bacteria and the first identification of a diterpene synthase and biosynthetic gene cluster responsible for the construction of the eunicellane scaffold. 

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4. Identification of the Biosynthetic Gene Cluster for the Organoarsenical Antibiotic Arsinothricin

   https://doi.org/10.1128/Spectrum.00502-21  

   Galván, Adriana E.; Paul, Ngozi P.; Chen, Jian; Yoshinaga-Sakurai, Kunie; Utturkar, Sagar M.; Rosen, Barry P.; Yoshinaga, Masafumi (September 2021, Microbiology Spectrum)

   Tang, Xiaoyu (Ed.)

   ABSTRACT The soil bacterium Burkholderia gladioli GSRB05 produces the natural compound arsinothricin [2-amino-4-(hydroxymethylarsinoyl) butanoate] (AST), which has been demonstrated to be a broad-spectrum antibiotic. To identify the genes responsible for AST biosynthesis, a draft genome sequence of B. gladioli GSRB05 was constructed. Three genes, arsQML , in an arsenic resistance operon were found to be a biosynthetic gene cluster responsible for synthesis of AST and its precursor, hydroxyarsinothricin [2-amino-4-(dihydroxyarsinoyl) butanoate] (AST-OH). The arsL gene product is a noncanonical radical S -adenosylmethionine (SAM) enzyme that is predicted to transfer the 3-amino-3-carboxypropyl (ACP) group from SAM to the arsenic atom in inorganic arsenite, forming AST-OH, which is methylated by the arsM gene product, a SAM methyltransferase, to produce AST. Finally, the arsQ gene product is an efflux permease that extrudes AST from the cells, a common final step in antibiotic-producing bacteria. Elucidation of the biosynthetic gene cluster for this novel arsenic-containing antibiotic adds an important new tool for continuation of the antibiotic era. IMPORTANCE Antimicrobial resistance is an emerging global public health crisis, calling for urgent development of novel potent antibiotics. We propose that arsinothricin and related arsenic-containing compounds may be the progenitors of a new class of antibiotics to extend our antibiotic era. Here, we report identification of the biosynthetic gene cluster for arsinothricin and demonstrate that only three genes, two of which are novel, are required for the biosynthesis and transport of arsinothricin, in contrast to the phosphonate counterpart, phosphinothricin, which requires over 20 genes. Our discoveries will provide insight for the development of more effective organoarsenical antibiotics and illustrate the previously unknown complexity of the arsenic biogeochemical cycle, as well as bring new perspective to environmental arsenic biochemistry. 

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5. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity

   https://doi.org/10.1128/aem.00600-24  

   Harper, Christopher P; Day, Anna; Tsingos, Maya; Ding, Edward; Zeng, Elizabeth; Stumpf, Spencer D; Qi, Yunci; Robinson, Adam; Greif, Jennifer; Blodgett, Joshua AV (May 2024, Applied and Environmental Microbiology)

   Reguera, Gemma (Ed.)

   ABSTRACT Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.<bold>IMPORTANCE</bold>Polycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, includingStreptomycesandLysobacterspp.Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity. 

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