Microbial Natural Products and Biosynthesis

A New Enzyme Family Catalyzing Methyllanthionine Sulfoxide Formation in Anti-phage Lanthipeptides

The paper identifies CoiH as an enzyme that catalyzes the formation of a sulfoxide group in methyllanthionine of anti-phage lanthipeptides.

MALDI Tandem Mass Spectrometry for Colony-Based Dereplication of Natural Products

This paper integrates MALDI-MS/MS into a bioinformatics platform to enable rapid metabolite annotation and strain prioritization from microbial colonies.

Uncovering bioactive metabolites from the Taxus wallichiana endophyte Annulohypoxylon purpureonitens using reverse metabolomics

This study identifies bioactive metabolites from the endophytic fungus Annulohypoxylon purpureonitens using metabolomics and bioactivity screening, revealing compounds with antibacterial, antioxidant, and cytotoxic properties.

Sequence-Derived Representations versus Pfam-Domain Content for Biosynthetic Gene Cluster Retrieval

The paper compares sequence-derived representations and Pfam-domain content for retrieving biosynthetic gene clusters, finding that Pfam remains the dominant signal.

Putative Herbicolin A, an antifungal lipopeptide produced by Pantoea agglomerans APC 4211 is a promising biocontrol agent against food spoilage fungi

This paper identifies herbicolin A, an antifungal lipopeptide from Pantoea agglomerans, as a promising natural biocontrol agent with low cytotoxicity and stability against food spoilage fungi.

Microbial bioprospecting for benzoxazolinate-like molecules: unleashing the potential of genome mining

The paper identifies 277 putative biosynthetic gene clusters for benzoxazolinate-like molecules through genome mining and presents a neural network model for detecting rare BGCs.

An Oligomeric Lanthipeptide from Nostoc punctiforme Promotes Host Association During Early Symbiosis with Blasia pusilla

This study identifies a lanthipeptide, nostolanthin, that promotes symbiosis between Nostoc punctiforme and Blasia pusilla through oligomerization.

A widespread Actinobacterial G Protein System regulates production of specialized metabolites in Streptomyces coelicolor

This study investigates the role of the Cvn8 AGPS in regulating specialized metabolite production in Streptomyces coelicolor using phylogenetic analysis and metabolomics.

Differentiating 5-thiooxazoles from oxazolone-coupled thioamides in RiPP natural products

The paper differentiates 5-thiooxazoles from oxazolone-coupled thioamides in RiPP natural products using chemical and structural analysis of oxazolin and methanobactin.

Computational pipeline reveals nature's untapped reservoir of halogenating enzymes

The paper develops a computational pipeline and database to annotate halogenating enzymes in genomic and metagenomic data, revealing underexplored clusters and improving predictions of microbial halogenated natural products.

Genome Mining of the Tumor Microbiome Reveals Biosynthetic Diversity and Potential Tumor-modulating Metabolites

The paper surveys the biosynthetic potential of the human tumor microbiome, identifying novel metabolites and their potential roles in tumor pathology.

Unconventional biocatalytic strategies orchestrate synthesis of the nucleoside analog sinefungin

This paper identifies and characterizes the sinefungin biosynthetic gene cluster, revealing unconventional biocatalytic strategies involving a B12-dependent radical SAM enzyme and PEARLs for nucleoside modification.

Identification of Siderophores with Unexpected Antibacterial Properties from Actinoplanes teichomyceticus

This study identifies siderophores from Actinoplanes teichomyceticus with antibacterial properties, showing activity against Gram-positive bacteria through a metal-dependent mechanism.

Unveiling the taxonomic diversity and unprecedented biosynthetic treasure of the phylum Myxococcota

The paper presents 154 new Myxococcota genomes, expands taxonomy, and identifies novel natural products, highlighting their biosynthetic potential for drug discovery.

Fine-Grained Structural Classification of Biosynthetic Gene Cluster-Encoded Products

The paper introduces BGCat, a machine learning tool for fine-grained classification of biosynthetic gene cluster-encoded products, improving upon existing methods and labeling over 100k BGCs.

Biosynthetic diversity and antifungal potential of soil-derived Saccharomonospora strains

This study evaluates the antifungal potential and biosynthetic diversity of Saccharomonospora strains, identifying novel bioactive metabolites and uncharacterized gene clusters.

Discovery of a phenazine thiol conjugase from sparse data using genome-informed machine learning

The paper uses genome-informed machine learning to discover a new enzyme, PTC, that catalyzes phenazine thioconjugation from sparse data.

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

metaSMASH improves BGC detection in large metagenomes by reducing computational cost while maintaining result accuracy.

The evolutionary processes of bacterial aromatic polyketide ketosynthases

The paper uses a protein language model to analyze the evolutionary history of bacterial aromatic polyketide ketosynthases and chain length factors, identifying a shared ancestral cluster and distinct evolutionary paths.

Bis-hydroxylation of Homocitrulline Catalyzed by a Multinuclear Nonheme Iron-Dependent Oxidative Enzyme during RiPP Biosynthesis

The paper identifies a novel RiPP biosynthetic pathway in Streptomyces thermodiastaticus involving a YcaO-TfuA pair, a carbamoyltransferase, and a MNIO enzyme that bis-hydroxylates homocitrulline.

BGX: A Comprehensive Pipeline for Genomic Insight into Bioactivity Prediction, Genomic Surveillance, and Novel Biosynthetic Gene Cluster Assessment

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

An activity-resistance tradeoff constrains enzyme evolution

This paper investigates the evolutionary tradeoff between enzyme activity and resistance to mycophenolic acid (MPA) and finds that resistance correlates with reduced catalytic efficiency across both ancestral and extant enzymes.

Reprogramming protein interfaces between adenylation and carrier protein domains in nonribosomal peptide synthetases

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

The "dark magic mushroom" co-produces amatoxins and psilocybin

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

Bacterial Geosmin Biosynthesis is Compartmentalized Inside a Two-Component Protein Shell

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.

A family of lanthipeptides with anti-phage function

The paper identifies a family of over 2000 lanthipeptide biosynthetic gene clusters in Actinobacteria with anti-phage function, demonstrating their conservation and novel compound production.

Identification of type III polyketide synthases from Ginger for dehydrogingerdione and curcumin biosynthesis by engineered Escherichia coli

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.

Total Biosynthesis of Pseudomonas aeruginosa-Derived Azabicyclocarbamates Identifies Distinct Dehydrating Condensation Family Proteins

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

Genetic dissection of persiathiacin biosynthesis defines hierarchical P450 oxidations and reveals a more potent antitubercular intermediate

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

Development of a High-throughput in vivo Assay for the Determination of Adenylation Domain Specificities

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.