Microbial Natural Products and Biosynthesis

BGX is a pipeline for genomic analysis that integrates tools for antimicrobial resistance profiling, biosynthetic gene cluster detection, and bioactivity prediction across microbial genomes.

This study reprograms protein interfaces between adenylation and carrier protein domains in NRPSs to enable non-cognate pairings and enhance natural product production.

The paper shows that Galerina indica produces both psilocybin and amatoxins, revealing horizontal gene transfer of psilocybin biosynthesis.

This study identifies a two-component Family 2B encapsulin shell that compartmentalizes geosmin synthase, showing its role in enzyme activity and stability through cargo loading peptides and pore conformation changes.

The paper identifies two DCS/PKS pairs in ginger that synthesize curcumin and 6-dehydrogingerdione, showing one can act as a dual-function enzyme for both products.

The paper identifies a new family of dehydrating condensation domain proteins involved in the biosynthesis of azabicyclocarbamates in Pseudomonas aeruginosa.

The paper identifies the enzymatic steps in persiathiacin biosynthesis, revealing a hierarchical sequence of P450-mediated modifications and a more potent antitubercular intermediate.

The paper develops an in vivo assay called ASCR to determine adenylation domain specificities in NRPS, testing 54 A domains from various organisms and confirming novel cyclic pentapeptides.

This study uses NRPS engineering to generate novel peptides with a pyrrolizixenamide moiety but finds that TE domain specificity limits further diversification.

The paper introduces non-canonical amino acids into non-ribosomal peptides by engineering NRPS systems and performing post-enzymatic chemical synthesis in bacterial culture extracts.

The paper identifies WARPs, cyclic non-ribosomal peptides, as structural determinants of fungal hydrophobicity, showing their role in maintaining surface hydrophobicity and aerial hyphae integrity.

The paper investigates the distribution, diversity, and metabolic potential of Myxococcota bacteria across Danish environments using metagenomic data, revealing their ecological roles and biotechnological potential.

This study identifies a frameshift mutation in M. extorquens AM1 that drives the production of methylolanthanin instead of rhodopetrobactin by altering the biosynthetic pathway.

This paper introduces BGC-MLM, a foundation model pretrained on biosynthetic gene clusters to predict molecular properties, bioactivity, and structural similarity, outperforming models without pretraining.

This study investigates how soil bacteria biotransform the antimicrobial peptide nisin, revealing its role in microbial nutrient recycling and community dynamics.

The paper investigates claims of N-deoxyschizokinen A production by Methylobacterium extorquens AM1 and concludes the detection is an artifact.

This study uses advanced microscopy to show that antibiotic biosynthesis in Streptomyces sp. Mg1 is integral to cell envelope structure and dynamics.

This study identifies the complete biosynthetic pathway of camptothecin, discovers missing enzymes, and validates the pathway through heterologous reconstruction in yeast.

BGC-QDR is a quantum-assisted pipeline for discovering and ranking biosynthetic gene clusters from eDNA, achieving 0.789 accuracy and 0.835 ROC-AUC using a variational quantum classifier.

This paper identifies KpbH as a PLP-dependent enzyme that catalyzes a decarboxylative Mannich-type reaction to construct a nonpeptidic scaffold in Kaitocephalin biosynthesis.

This study investigates the substrate promiscuity of the enzyme HphB in the homologation pathway, showing it can accept diverse side chains while maintaining backbone specificity.

The paper identifies compact, data-driven codes for adenylation domain substrate specificity in NRPSs, outperforming traditional codes and revealing new positions critical for specificity.

novelBGC assesses BGC novelty and prioritizes candidates using two scores, outperforming single-axis tools in identifying novel clusters.

This study analyzes 1432 transcriptomics datasets from 132 Actinomycetota strains to identify patterns of BGC expression and regulatory mechanisms.

RetroMol converts natural product structures and biosynthetic gene clusters into shared primary sequences to enable biosynthetic similarity comparisons.

This study isolates and characterizes new lysolipin analogues from Streptomyces sp. P8-2B18, revealing structural diversity and varying bioactivities against bacteria, fungi, and cancer cells.

The study identifies pavettamine, a toxin causing gousiekte in livestock, as being synthesized by bacterial endophytes via a conserved gene cluster acquired through horizontal gene transfer.

The paper constructs a regulatory atlas of Streptomyces and related actinomycetes using DAP-seq and ChIP-seq, revealing conserved and divergent transcriptional networks.

The paper links gene clusters in Floridanema to the production of β-amino polyketide residues, revealing shared biosynthetic architectures and evolutionary strategies.

The paper presents a CURE model that identifies bacterial isolates producing bioactive metabolites antagonizing the C. elegans Ras signaling pathway through phenotype suppression.