Microbial Natural Products and Biosynthesis

Identification of potential colorectal-cancer-protective bioactive natural compounds in the human gut microbiome

The paper identifies four BGCs enriched in healthy individuals and one linked to a curacin-A-like metabolite, suggesting potential CRC-protective compounds from the gut microbiome.

Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species

This study identifies a novel family of bacitracin-type antibiotics, paenitracins, produced by Paenibacillus species using a metabolomics-genomics workflow.

Biosynthesis of 14-membered cyclopeptide alkaloids via non-heme-iron- and 2-oxoglutarate-dependent oxidative decarboxylation

This study identifies the biosynthetic pathway for a 14-membered cyclopeptide alkaloid, lotusine A, involving non-heme-iron and 2-oxoglutarate-dependent oxidative decarboxylation and SAM-dependent N-terminal methylation.

DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides

DeepHalo uses deep learning to identify halogenated metabolites from mass spectrometry data, discovering new cyclic depsipeptides with antibacterial activity.

Comparative genomics analysis reveals that antimicrobial activity in Pseudomonas protegens PBL3 is associated with gene clusters participating in multiple cellular functions

This study identifies gene clusters in Pseudomonas protegens PBL3 associated with antimicrobial activity against Burkholderia glumae using comparative genomics.

Artificial Recombination of Nonribosomal Peptide Synthetases Rapidly Evolves Natural Products

The paper introduces RACE, a method for rapidly evolving NRPSs through recombineering, generating novel peptides and uncovering new recombination sites.

Biosynthesis of Kaitocephalin: A Neuroprotective Natural Product Featuring a Peptide-Like yet Non-Peptidic Scaffold

This paper identifies the biosynthetic gene cluster for kaitocephalin in Eupenicillium shearii and characterizes key enzymes involved in its unique non-peptidic scaffold formation.

LoReMINE: Long Read-based Microbial genome mining pipeline

LoReMINE is an automated pipeline for microbial genome mining that integrates assembly, classification, and biosynthetic gene cluster prediction from long-read data.

Chemical capture of diazo metabolites reveals biosynthetic hydrazone oxidation

The paper develops a reactivity-based screening method to capture diazo-containing metabolites, discovering two novel compounds from Nocardia ninae and revealing their biosynthesis via hydrazone oxidation catalyzed by Dob3.

Chromid-like secondary replicons as key sites of biosynthetic gene clusters in Ktedonobacteria

The paper identifies chromid-like secondary replicons in Ktedonobacteria as key genomic regions harboring biosynthetic gene clusters, expanding understanding of soil microbial secondary metabolism.

An antifungal with a novel mechanism of action discovered via resistance gene-guided genome mining

This study identifies a novel antifungal compound targeting ALS, validated through genome mining, biochemical assays, and a mouse model of invasive aspergillosis.

Biocontrol efficacy of 2-pyrroldione-5-carboxylic acid (2Py-5CA), an antifungal bioactive macromolecule from the endophyte Penicillium oxalicum, against Ramularia collo-cygni in barley

This study identifies 2Py-5CA, an antifungal compound from Penicillium oxalicum, as effective against Ramularia leaf spot in barley.

Integrated metabolomic and genomic insights into amino acid incorporation within the hybrid polyketide-alkaloid antibiotic TLN-05220

This study identifies enzymes involved in amino acid incorporation into the antibiotic TLN-05220 using metabolomic and genomic analyses.

Biocatalytic Tetrapeptide Macrocyclization by Cryptic Penicillin-binding Protein-type Thioesterases

This paper discovers a thioesterase enzyme, WP516, capable of efficiently cyclizing a wide range of tetrapeptides, expanding the scope of biocatalytic methods for cyclic tetrapeptide synthesis.

Biosynthetic gene clusters everywhere, but the environment selects

The study investigates BGC diversity and activity in peatland soils, finding that environmental factors influence which BGCs are expressed.

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

The paper introduces updated versions of BiG-SCAPE and BiG-SLiCE for improved analysis of metabolic gene clusters, showing they provide consistent estimates of gene cluster diversity.

Structural Basis for Iterative Methylation by a Cobalamin-dependent Radical S-Adenosylmethionine Enzyme in Cystobactamids Biosynthesis

This paper reports X-ray crystal structures of a cobalamin-dependent radical S-adenosylmethionine enzyme, revealing how it facilitates iterative methylation of substrates and cobalamin.

Oxidative Peptide Backbone Cleavage by a HEXXH Enzyme During RiPP Biosynthesis

This study identifies two HEXXH enzymes that catalyze oxidative backbone cleavage in RiPP biosynthesis by recognizing specific peptide motifs.

Covalent Leader Peptide Probes Enable Proteome-Level Mapping of RiPP Enzymes beyond Biosynthetic Gene Clusters

This study develops covalent leader peptide probes to identify RiPP enzymes outside biosynthetic gene clusters, revealing cross-cluster enzymatic interactions.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Structures and broad-spectrum growth-inhibiting activity of formomarinobactin, formylated marinobactin analogues from the Pseudomonas lutea clade

This study characterizes formomarinobactin, a novel siderophore from Pseudomonas lutea clade, showing its role in iron acquisition and broad-spectrum microbial growth inhibition.

Using a "one-strain-many-compounds" (OSMAC) approach to screen a collection of diverse fungi from Aotearoa New Zealand for antibacterial activity against Escherichia coli

The paper screens 32 New Zealand fungi for antibacterial activity against E. coli using OSMAC, finding several active isolates and highlighting media effects on bioactivity.

Efficient in vitro refactoring and biosynthetic gene cluster amplification for the overproduction and accelerated discovery of anticancer thioamitides

The paper describes methods to enhance thioalbamide production by refactoring its biosynthetic gene cluster and identifies a related compound with anticancer activity.

A transcriptional regulator gene TRG1 of Trichoderma longibrachiatum is involved in the regulation of peptaibols synthesis

This study identifies TRG1 as a key transcriptional regulator essential for peptaibol biosynthesis in Trichoderma longibrachiatum, showing reduced peptaibol production in a gene knockout mutant.

The one that abstained: Psilocybe fuscofulva genome suggests two recent origins of the psilocybin gene cluster in Psilocybe

This study identifies two independent origins of the psilocybin gene cluster in Psilocybe by analyzing genome sequences and phylogenetic relationships.

The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries

The paper analyzes BGCs in oral microbiome metagenomic and metatranscriptomic data to identify their abundance and association with health and dental caries.

Switching Metazoan Fatty Acid Synthase Between Reducing and Non-reducing Elongation Mode via Programming of the Ketoreductase Domain

This study engineers metazoan fatty acid synthase to switch from reducing to non-reducing elongation mode by modifying the ketoreductase domain, producing pyrone intermediates.

An integrative genomic and chemical similarity approach linking fungal secondary metabolites and biosynthetic gene clusters

The paper links fungal secondary metabolites to their biosynthetic gene clusters using genomic and chemical similarity, identifying 22 known pairs and hypothesizing 38 others in Aspergillus fischeri.

A biocatalytic platform for the production of substituted 2-quinolones and (thio)coumarins

This paper characterizes two fungal polyketide synthases that produce substituted 2-quinolones and (thio)coumarins, demonstrating their potential for biocatalytic drug discovery.

Selective labeling supports 5-thiooxazole post-translational modification in bufferins

The paper identifies 5-thiooxazoles as the cysteine post-translational modifications in bufferins using isotopic labeling and confirms consistency with related MNIO families.