Microbial Natural Products and Biosynthesis

DiscERN: An Automated Genome Mining Tool for the Discovery of Evolutionarily Related Natural Products

DiscERN is a tool for discovering evolutionarily related natural products by analyzing genomes, validated by isolating a new antibiotic.

Derivatization of the non-ribosomal peptide pyrrolizixenamide using NRPS engineering

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

Site-Specific Introduction of Non-Canonical Amino Acids into natural and engineered Non-Ribosomal Peptides

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.

Non-ribosomal Peptides as Structural Determinants of Fungal Hydrophobicity

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.

From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments

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.

Structure and activity of class II lanthipeptides from a thermophilic bacterium

The paper identifies and structurally analyzes two class II lanthipeptides from a thermophilic bacterium, revealing deviations in thioether ring formation and demonstrating antimicrobial activity.

A frameshift mutation drives divergent biosynthesis of metallophores in Methylobacterium extorquens

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

A foundation model enables prediction of natural product molecular properties, bioactivity, and structural similarity from biosynthetic gene cluster sequence

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.

Beyond Antimicrobial Activity: Soil Bacteria Reveal a Biotransformation Fate for the Lanthipeptide Nisin

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

There is no convincing evidence that Methylobacterium extorquens AM1 can produce N-deoxyschizokinen A

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

DeepAden: an explainable machine learning for substrate specificity prediction in nonribosomal peptide synthetases

DeepAden predicts A-domain substrate specificities in NRPSs using a two-stage deep learning framework, achieving competitive performance and enabling the identification of novel NRP gene clusters.

Molecular basis for depsipeptide HDAC inhibitor combinatorial biosynthesis

The paper identifies a novel subunit docking mechanism in depsipeptide HDAC inhibitor biosynthesis using gene proximity searching and experimental validation.

Direct fluorescence detection and volume electron microscopy reveal a role for antibiotic biosynthesis in the bacterial cell envelope of Streptomyces sp. Mg1

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

Complete elucidation and heterologous reconstruction of the biosynthetic pathway of camptothecin

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

Nerpa 2: probabilistic linking of biosynthetic gene clusters to nonribosomal peptides

Nerpa 2 links biosynthetic gene clusters to nonribosomal peptides using probabilistic models, improving accuracy and scalability in pathway reconstruction.

AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde

The paper identifies three new cyclic depsipeptides from a marine cyanobacterium using AI tools and metabolomics, showing their antiplasmodial activity and structural diversity.

BGC-QDR: A Quantum-Assisted Pipeline for Biosynthetic Gene Cluster Discovery and Ranking from Environmental DNA

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.

Substrate scope and catalytic mechanism of α, β-epoxyketone synthase EpnF illuminated by in-situ esterase-mediated deprotection

This paper develops an esterase-mediated strategy to generate unstable substrates for EpnF, revealing its broad substrate tolerance and catalytic mechanism for epoxyketone synthesis.

Discovery and Biosynthesis of Nitrilobacillins by Post-translational Introduction of C-Terminal Nitrile Groups

The paper identifies and characterizes a RiPP biosynthetic gene cluster that introduces nitrile groups via an AS-like enzyme, expanding knowledge of RiPP structural diversity and enzymatic versatility.

A PLP-Dependent Decarboxylative Mannich Reaction Initiates Construction of the Nonpeptidic Scaffold of Kaitocephalin

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

High side chain promiscuity of the terminal enzyme in the homologation pathway for L-phenylalanine and L-tyrosine

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.

Investigating the versatility of cytochalasan cytochrome P450 monooxygenases using combinatorial biosynthesis reveals stereochemical restrictions

This study uses combinatorial biosynthesis to investigate P450 enzymes involved in cytochalasan biosynthesis, revealing stereochemical restrictions in their substrate specificity.

A data-driven rediscovery of the specificity-conferring code of adenylation domains in nonribosomal peptide synthetases

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: An interactive dual-score framework for biosynthetic gene cluster novelty assessment and candidate prioritisation

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

Toward understanding drivers of specialized metabolism in Actinomycetota: insights from 1432 transcriptomics datasets for 132 strains

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

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

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

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes

PhyloNaP provides a database of phylogenetic trees for biosynthetic enzymes, enabling functional inference and community contributions.

Antimicrobial and Cytotoxic Lysolipins I-M Isolated from Streptomyces sp. P8-2B18

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.

A fatal plant toxicosis described more than a century ago is caused by a bacterial endophyte

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.

A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

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