Microbial Natural Products and Biosynthesis

The paper uses transporter gene frequencies to predict metabolite characteristics and identifies siderophore-like BGCs in gut microbiomes.

The paper demonstrates the heterologous expression of two cyclic pentapeptide families from Streptomyces cacaoi CA-170360, showing their biosynthesis by two nonribosomal peptide synthetases and a Penicillin Binding Protein enzyme.

BiG-SLiCE clusters 1.2 million biosynthetic gene clusters from microbial genomes and MAGs efficiently, enabling analysis of secondary metabolic diversity and novel chemistry.

This study engineers the biosynthesis of the polyketide bikaverin in yeast by enhancing enzyme expression and using enzyme fusion to increase yield.

This paper identifies a novel melanin biosynthetic pathway in Ustilago maydis involving multiple polyketide synthases and other enzymes, distinct from known fungal melanin pathways.

This paper develops genetic tools for heterologous expression of biosynthetic gene clusters in cyanobacteria, enabling high-titer production of cryptomaldamide in Anabaena.

The paper demonstrates that substituting adenylation domains in NRPS enzymes can generate novel non-ribosomal peptides, challenging previous assumptions about substrate specificity.

The paper engineers bimodular PKS systems to produce unnatural polyketides as bio-based chemicals, demonstrating both successes and challenges in product fidelity.

RRE-Finder identifies RRE domains across RiPP biosynthetic gene clusters, discovering novel classes and providing a dataset for further biochemical study.

The paper identifies SM gene clusters in non-Dikarya fungi, particularly Basidiobolus, and shows horizontal gene transfer contributes to SM diversification in amphibian gut symbionts.

This study identifies and characterizes the biosynthetic pathway for alkylcitric acids in Aspergillus niger using genomic analysis and experimental overexpression.

The paper introduces PKSpop, a coevolution-based method to predict protein-protein interactions in PKS assembly lines, achieving 80% accuracy in predicting protein order.

A dLbCas12a-VPR CRISPR activation system works in Aspergillus nidulans, boosting microperfuranone output from the native micA gene and revealing dehydromicroperfuranone as the mic cluster product.

The paper mines over 100,000 genomes to identify 8,500 lanthipeptide precursor peptides, revealing their broader distribution and diversity across bacterial and archaeal phyla.

The paper identifies novel biosynthetic gene clusters in Dothideomycetes fungi and shows their diversity scales with repertoire size, suggesting limited structural redundancy in secondary metabolites.

The paper describes a Penicillium rubens strain with reduced secondary metabolite production, used to efficiently express a polyketide gene cluster for high-yield metabolite production.

The paper introduces two tools, BiG-SCAPE and CORASON, for analyzing biosynthetic gene clusters in large genomic datasets, demonstrating their utility through validation and discovery of new gene cluster families.

The paper analyzes gene cluster diversity in Fusarium fungi, identifying processes like horizontal transfer and transposable element-driven rearrangements that shape specialized metabolite production.

NeuRiPP improves identification of RiPP precursor peptides by using neural networks trained on diverse datasets, outperforming existing tools in detecting novel RiPP classes.

DDAP predicts biosynthetic pathways of type I PKS by improving module docking domain ordering and affinity prediction, achieving AUC 0.88 and MRR 0.67.

This paper introduces DeepBGC, a deep learning method for improved biosynthetic gene cluster prediction, uncovering previously undetectable clusters with potential novel biological activities.

This paper describes a method to modify and design non-ribosomal peptide synthetases (NRPSs) using a new fusion point in condensation domains to produce peptides, including non-natural amino acids, at high yields.

The paper develops a pipeline to identify putative resistance genes in biosynthetic gene clusters across fungal genomes, validating it with known resistance genes.

The paper investigates the role of AbsA2 in antibiotic biosynthesis in Streptomyces coelicolor by analyzing gene expression and DNA-binding sites in a deletion mutant.

EvoMining analyzes enzyme family expansion and recruitment in prokaryotes to identify novel natural product biosynthetic systems and their evolutionary origins.

This study uses CRISPR/Cas9 to activate a silent gene cluster in Streptomyces sclerotialus, leading to the discovery of scleric acid and its biosynthetic pathway.

A yeast-based refactoring platform (HEx) with new inducible promoters, an engineered host strain, and homology-based assembly expressed 41 cryptic fungal gene clusters; 22 yielded non-native compounds.

The paper identifies secondary metabolite clusters from lake metagenomes using improved binning and analysis tools.

The paper identifies a novel cytochrome P450 enzyme involved in clifednamide biosynthesis and demonstrates its use in engineering Streptomyces strains to produce clifednamides.

This study identifies five types of genetic variation in secondary metabolic gene clusters across 66 strains of Aspergillus fumigatus and links them to evolutionary drivers like mutation, recombination, and horizontal gene transfer.