Microbial Natural Products and Biosynthesis

Directed Evolution of a Pantoea Strain for Antibiotic Production via Interspecies Competition: A Reproducible Experimental Approach

This paper describes a method to evolve antibiotic-producing Pantoea strains through interspecies competition and temperature stress, resulting in reproducible strain-specific antibiotic activity.

Assessing substrate scope of the cyclodehydratase LynD by mRNA display-enabled machine learning models

This paper uses mRNA display and machine learning to predict substrate promiscuity of the RiPP cyclodehydratase LynD and identify epistatic interactions.

Discovery and description of gammanonin: a widely distributed natural product from Gammaproteobacteria

This paper identifies gammanonin, a natural product from Gammaproteobacteria that inhibits bacterial peptide deformylase without the toxic hydroxamate group found in actinonin.

Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi

This study shows that co-culturing xylarialean fungi increases metabolite diversity and bioactivity, suggesting competitive interactions drive secondary metabolism.

Identification and biosynthesis of xildivaline, a novel and widespread peptide deformylase inhibitor from Gammaproteobacteria

The paper identifies xildivaline, a novel peptide deformylase inhibitor produced by Gammaproteobacteria, and elucidates its biosynthesis and structural features.

Polyketide synthase-derived sphingolipids determine microbiota-mediated protection against pathogens in C. elegans

The paper identifies sphingolipids from a bacterial PKS as mediators of microbiota protection against pathogens in C. elegans.

Changing the initiation unit of nonribosomal peptide synthetases to access underexplored biosynthetic potential

This paper introduces a strategy to activate silent NRPS biosynthetic gene clusters by swapping initiation units, successfully recovering three of six previously silent pathways and identifying five novel lipopeptides.

A new heme enzyme family forms hydrazine groups in diverse biosynthetic pathways

This paper identifies a new heme enzyme family that catalyzes hydrazine formation in natural product biosynthesis through a four-electron reduction of nitrite.

Association of secondary metabolite gene clusters with host-specific lineages of the cereal blast fungus Pyricularia oryzae

The paper identifies secondary metabolite gene clusters in Pyricularia oryzae lineages associated with host specialization and virulence.

Discovery and Biosynthesis of Sulfenicin and Its New-to-Nature Acylsulfenic Acid Functional Group

The paper discovers sulfenicin, a novel natural product with a unique acylsulfenic acid functional group, and identifies the enzymes involved in its biosynthesis.

Discovery of lydiamycin A biosynthetic gene cluster in the plant pathogen Rhodococcus fascians guides structural revision and identification of molecular target

The paper identifies a biosynthetic gene cluster in Rhodococcus fascians that produces lydiamycin A, a novel HPS-containing macrocyclic pentapeptide with antibacterial activity against peptide deformylase.

Characterization of a novel glycocin from a thermophile

This study characterizes thermoglycocin, a novel glycocin from Thermoanaerobacterium thermosaccharolyticum, with three disulfide bonds, O- and S-GlcNAcylation, and a unique C39 protease cleavage site.

Discovery and Biosynthetic Origin of 4,4'-Dihydroxy-3,3',5,5' Tetrachlorobenzophenone Produced by the Clinical Isolate Burkholderia oklahomensis

The paper identifies a novel polychlorinated compound produced by Burkholderia oklahomensis and proposes its biosynthetic pathway.

Fast, flexible gene cluster family delineation with IGUA

IGUA is a fast and scalable method for delineating gene cluster families in prokaryotic genomes, outperforming existing tools in speed without sacrificing accuracy.

Lydicamycins Induce Morphological Differentiation in Actinobacterial Interactions

This study identifies lydicamycins as inducers of morphological differentiation in actinobacterial interactions using co-cultivation and multi-omics approaches.

An O-acetylated derivative of piericidin A1 produced by Kitasatospora sp. A2-31 has potent activity against the cacao mirid bug, Helopeltis bakeri Poppius

The paper identifies a novel acetylated derivative of piericidin A1 from Kitasatospora sp. A2-31 that shows 100% mortality against the cacao mirid bug.

Siderophores can alter the population dynamics of fungal-bacterial communities by inhibiting specialized metabolism

This study shows bacillibactin inhibits Penicillium specialized metabolism by causing iron deficiency, altering fungal-bacterial community dynamics.

Biosynthetic characterization and combinatorial biocatalysis of the cysteine protease inhibitor E-64

This study characterizes the biosynthesis of E-64, a cysteine protease inhibitor, and demonstrates its biocatalytic potential for generating potent analogs.

Tracing Siderophore Precursors to Primary Metabolism for Ecological Applications

The paper develops a framework to trace siderophore biosynthesis to primary metabolism and applies it to identify metabolic differences between beneficial and pathogenic bacteria.

Uncovering Microbial Biosynthetic Potential with Genomic Context-aware Protein Language Model

BGC-Finder uses protein language models to detect and annotate biosynthetic gene clusters in microbial genomes and metagenomes, improving speed and detection of core genes and cytochrome P450s.

Influence of rifampicin-resistance mutations on the synthesis of antioxidant, DNA-protective, and SOS-inhibitory metabolites

This study examines how rifampicin-resistance mutations in Bacillus strains affect the synthesis of antioxidant, DNA-protective, and SOS-inhibitory metabolites, finding increased activity in resistant mutants.

The emergence and loss of cyclic peptides in Nicotiana illuminate dynamics and mechanisms of plant metabolic evolution

This paper resurrects an extinct burpitide cyclase from Nicotiana attenuata, revealing its evolutionary origin and function in producing novel cyclic peptides.

Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho-Tyrosines

This study identifies a conserved FHAFRF-motif in precursor peptides of MNIO-encoding BGCs and demonstrates that MNIO and B12-rSAM enzymes catalyze ortho-hydroxylation and crosslinking of phenylalanine residues to form macrocyclic peptides.

Deciphering the Biosynthetic Potential of Microbial Genomes Using a BGC Language Processing Neural Network Model

This paper introduces BGC-Prophet, a transformer-based model for identifying and extrapolating biosynthetic gene clusters (BGCs) in microbial genomes and metagenomes, revealing evolutionary patterns and enhancing BGC discovery.

Decoding the chemical language of RiPPs from the untapped Archaea domain

This paper identifies twenty-four new archaeal lanthipeptides with unique chemical features and ecological functions, expanding the known chemical diversity of archaeal secondary metabolites.

Genomic characterization and enhanced fermentation of the endophyte Stemphylium sp. (Aa22), a producer of bioactive alkyl-resorcinols

This paper characterizes the genome of Stemphylium sp. Aa22, identifies a T3PKS gene for alkyl-resorcinol biosynthesis, and evaluates fermentation conditions to enhance bioactive compound production.

In vivo activation of the dia BGC allows consolidation of the biosynthetic pathways of diaporthin, dichlorodiaporthin, diaporthinic acid, and diaporthinol

This study activates the dia biosynthetic gene cluster in Trichoderma reesei, identifying diaporthinic acid as the primary metabolite and elucidating the roles of key genes in its biosynthesis.

Comprehensive Biosynthetic Analysis of Human Microbiome Reveals Diverse Protective Ribosomal Peptides

This study identifies diverse ribosomally synthesized peptides in the human microbiome and shows some inhibit pathogens and reduce inflammation.

AI-assisted isolation of bioactive Dipyrimicins from Amycolatopsis azurea and identification of its corresponding dip biosynthetic gene cluster

The paper uses a machine learning model to predict antibacterial activity from biosynthetic gene clusters, leading to the isolation of dipyrimicins A and B from Amycolatopsis azurea and linking them to their BGC.

Characterization of a marine bacteria through a novel metabologenomics approach

The paper characterizes a marine bacteria using a metabologenomics approach, linking genomic and metabolomic data to identify a new biosynthetic gene cluster and bioactive compound.