Microbial Natural Products and Biosynthesis

Specialization in Molecular Functions and Secondary Metabolite Production Potential in Cyanobacterial Symbionts

This study compares molecular functions and biosynthetic gene clusters in cyanobacterial genomes to identify specializations associated with symbiotic lifestyles.

The transcriptional regulator Lrp activates the expression of genes involved in tilivalline enterotoxin biosynthesis in Klebsiella oxytoca

The paper shows that Lrp activates aroX and npsA genes involved in tilivalline biosynthesis in K. oxytoca, reducing cytotoxicity in its absence.

Pangenome mining of the Streptomyces genus redefines their biosynthetic potential

The paper analyzes 2,371 Streptomyces genomes to refine biosynthetic gene cluster (BGC) diversity using MASH-clusters and reveals conserved genomic structures suggesting vertical inheritance.

Machine Learning Uncovers the Transcriptional Regulatory Network for the Production Host Streptomyces albidoflavus

The paper uses independent component analysis to characterize the transcriptional regulatory network of Streptomyces albidoflavus and identifies iModulons that describe its activity across growth conditions.

A flexible, modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

The paper develops a flexible DNA assembly toolkit for gene cluster engineering in Streptomyces to enhance natural product production.

Genome mining of Streptomyces for the discovery of low-resistance antibiotics

This study uses genomic analysis of Streptomyces to identify novel antimicrobial compounds with low resistance potential, leveraging bioinformatics tools and AI predictions.

Machine learning-based exploration, expansion and definition of the atropopeptide family of ribosomally synthesized and posttranslationally modified peptides

This study introduces AtropoFinder, a machine learning tool that identifies atropopeptide biosynthetic gene clusters and expands the known chemical diversity of this RiPP family.

ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome

ABC-HuMi catalogs 19,218 biosynthetic gene clusters from the human microbiome, offering a comprehensive resource for exploring bioactive compound potential.

Automated, self-resistance gene-guided, and high-throughput genome mining of bioactive natural products from Streptomyces

The paper introduces a high-throughput platform for discovering bioactive natural products from Streptomyces by combining computational prediction, cloning, and heterologous expression of biosynthetic gene clusters.

Genome Mining of Salinispora Uncovers a Repertoire of Secondary Metabolites and Carbohydrate-Active Enzymes

This study mines Salinispora genomes to identify secondary metabolite biosynthetic gene clusters and carbohydrate-active enzymes, revealing potential for new drug development.

A guidance into the fungal metabolomic abyss: Network analysis for revealing relationships between exogenous compounds and their outputs

The paper introduces network analysis methods to identify exogenous compounds that trigger specialized metabolite production in fungi and distinguish unknown analytes.

Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte - Alternaria burnsii NCIM 1409

This study analyzes the genome and transcriptome of the fungal endophyte Alternaria burnsii NCIM 1409 to understand camptothecin biosynthesis and its defense mechanisms.

Structural Basis of Streptomyces Antibiotic Regulatory Proteins Activating Transcription

This study reveals the molecular mechanism of SARP transcriptional activation using cryo-EM, showing how SAS interacts with DNA and RNAP to facilitate antibiotic biosynthesis.

Guidelines for Optimizing Type S Non-Ribosomal Peptide Synthetases

This paper introduces guidelines for optimizing type S non-ribosomal peptide synthetases to improve production yields of artificial non-ribosomal peptides.

CLOCI: Unveiling cryptic gene clusters with generalized detection

CLOCI identifies gene clusters using co-occurrence and orthology proxies, revealing noncanonical clusters and improving detection of known functional classes.

Directed evolution of piperazic acid incorporation by a nonribosomal peptide synthetase

The paper reports directed evolution of an NRPS adenylation domain to incorporate piperazic acid, demonstrating that low-throughput methods can alter NRPS substrate specificity.

Metagenomic domain substitution for the high-throughput modification of non-ribosomal peptide analogues

The paper uses metagenomic domain substitution to generate novel non-ribosomal peptides by screening over 1,000 domains in a pyoverdine NRPS, resulting in 16 distinct products.

Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS

This paper introduces SanntiS, a machine learning tool for identifying biosynthetic gene clusters in genomic and metagenomic data, and demonstrates its ability to predict a large number of novel BGCs with experimental validation.

Deep self-supervised learning for biosynthetic gene cluster detection and product classification

This paper introduces a self-supervised learning approach to detect and classify biosynthetic gene clusters in microbial genomes using masked language models trained on protein domains.

Knowledge-guided data mining on the standardized architecture of NRPS: subtypes, novel motifs, and sequence entanglements

The paper introduces a standardized NRPS architecture using conserved motifs, leading to new subtype classifications, novel motifs, and insights into reengineering challenges.

Discovery and biosynthetic assessment of Streptomyces ortus sp nov. isolated from a deep-sea sponge

This paper isolates a new Streptomyces species from a deep-sea sponge and identifies six unique biosynthetic gene clusters through comparative analysis.

CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters

CAGECAT enables rapid homology searches and visualization of gene clusters across genomes, aiding in the discovery of novel metabolites through comparative analysis.

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC

The paper introduces lsaBGC, a bioinformatics tool for analyzing BGCs in skin microbiomes, revealing evolutionary patterns and novel SNVs in key species.

Integration of microbial and chemical synthesis for the efficient production of plitidepsin, a promising anticancer and antiviral agent

This paper combines microbial and chemical synthesis to efficiently produce plitidepsin, achieving high yields and new analogues with anticancer and antiviral activities.

Bursts in biosynthetic gene cluster transcription are accompanied by surges of natural compound production in the myxobacterium Sorangium sp.

The paper shows that bursts in biosynthetic gene cluster transcription in Sorangium sp. correlate with natural compound production, challenging the idea that BGCs are preferentially expressed under nutrient limitation.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

The paper compares metabolic gene clusters and mycoparasitism genes in endophytic and non-endophytic Trichoderma genomes to uncover genomic features associated with the endophytic lifestyle.

Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

The paper classifies biosynthetic gene clusters in the Bacillus cereus group using manual and automated approaches, identifying conserved and novel clusters and proposing a classification framework.

Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis

This study uses population genomics to identify genetic targets for improving phenazine biosynthesis in Pseudomonas chlororaphis through genome-wide association analysis and experimental validation.

Structural and evolutionary analyses support reclassification of glycopeptide antibiotics as xyclopeptides

The paper reclassifies glycopeptide antibiotics as xyclopeptides based on structural and evolutionary analyses of biosynthetic gene clusters.

iPRESTO: automated discovery of biosynthetic sub-clusters linked to specific natural product substructures

iPRESTO detects sub-clusters in biosynthetic gene clusters to link natural product substructures to their genetic origins, improving annotation and discovery.