Mining genomes to illuminate the specialized chemistry of life

MH Medema, T de Rond, BS Moore - Nature Reviews Genetics, 2021 - nature.com
All organisms produce specialized organic molecules, ranging from small volatile chemicals
to large gene-encoded peptides, that have evolved to provide them with diverse cellular and …

Microbial chassis engineering drives heterologous production of complex secondary metabolites

J Liu, X Wang, G Dai, Y Zhang, X Bian - Biotechnology Advances, 2022 - Elsevier
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently
known secondary metabolites. Heterologous production of secondary metabolite BGCs in …

Precise DNA cleavage using CRISPR-SpRYgests

KA Christie, JA Guo, RA Silverstein, RM Doll… - Nature …, 2023 - nature.com
Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave
DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific …

Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach

M Liang, L Liu, F Xu, X Zeng, R Wang… - Nucleic Acids …, 2022 - academic.oup.com
Direct cloning of biosynthetic gene clusters (BGCs) from microbial genomes facilitates
natural product-based drug discovery. Here, by combining Cas12a and the advanced …

Genome mining unveils a class of ribosomal peptides with two amino termini

H Ren, SR Dommaraju, C Huang, H Cui, Y Pan… - Nature …, 2023 - nature.com
The era of inexpensive genome sequencing and improved bioinformatics tools has
reenergized the study of natural products, including the ribosomally synthesized and post …

Recent advances in genome mining and synthetic biology for discovery and biosynthesis of natural products

M Wang, L Chen, Z Zhang, Q Wang - Critical Reviews in …, 2025 - Taylor & Francis
Natural products have long served as critical raw materials in chemical and pharmaceutical
manufacturing, primarily which can provide superior scaffolds or intermediates for drug …

Biology and applications of CRISPR–Cas12 and transposon-associated homologs

WY Wu, B Adiego-Pérez, J van der Oost - Nature Biotechnology, 2024 - nature.com
CRISPR-associated Cas12 proteins are a highly variable collection of nucleic acid-targeting
proteins. All Cas12 variants use RNA guides and a single nuclease domain to target …

Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides

H Ren, C Huang, Y Pan, SR Dommaraju, H Cui, M Li… - Nature Chemistry, 2024 - nature.com
Recent efforts in genome mining of ribosomally synthesized and post-translationally
modified peptides (RiPPs) have expanded the diversity of post-translational modification …

Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces

A Ameruoso, MC Villegas Kcam, KP Cohen… - Nucleic Acids …, 2022 - academic.oup.com
The rise of antibiotic-resistant bacteria represents a major threat to global health, creating an
urgent need to discover new antibiotics. Natural products derived from the genus …

Multiplexed mobilization and expression of biosynthetic gene clusters

V Libis, LW MacIntyre, R Mehmood, L Guerrero… - Nature …, 2022 - nature.com
Bacterial genomes contain large reservoirs of biosynthetic gene clusters (BGCs) that are
predicted to encode unexplored natural products. Heterologous expression of previously …