Mining and unearthing hidden biosynthetic potential

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

(2021) Satria A Kautsar et al.   GigaScience

Genome mining of oxidation modules in trans-acyltransferase polyketide synthases reveals a culturable source for lobatamides

(2020) Reiko Ueoka et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Mining Symbionts of Spider-Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones

(2020) Sarah P. Niehs et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Targeted induction of a silent fungal gene cluster encoding the bacteria-specific germination inhibitor fumigermin

(2020) Maria Cristina Stroe et al.   eLife

Landornamides: Antiviral Ornithine‐Containing Ribosomal Peptides Discovered through Genome Mining

(2020) Nina M. Bösch et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation

(2020) Jian‐Ming Lv et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

(2020) Mehmet Direnç Mungan et al.   NUCLEIC ACIDS RESEARCH

A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli

(2020) Michael Rust et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy

(2020) Kyle L. Dunbar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts

(2020) Mathew A. Storey et al.   mBio

Chemical Mediators at the Bacterial-Fungal Interface

(2020) Kirstin Scherlach et al.   Annual Review of Microbiology

Structure and bioactivity of colibactin

(2020) Kevin M. Wernke et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Oak‐Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins

(2020) Keishi Ishida et al.   CHEMISTRY-A EUROPEAN JOURNAL

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

(2020) Alexander M. Kloosterman et al.   mSystems

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

(2020) Alexander M. Kloosterman et al.   PLOS BIOLOGY

SeMPI 2.0—A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases

(2020) Paul F. Zierep et al.   Metabolites

Genome-Mined Diels–Alderase Catalyzes Formation of the cis-Octahydrodecalins of Varicidin A and B

(2019) Dan Tan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria

(2019) Alex J. Mullins et al.   Nature Microbiology

rBAN: retro-biosynthetic analysis of nonribosomal peptides

(2019) Emma Ricart et al.   Journal of Cheminformatics

Opening up the Single-Cell Toolbox for Microbial Natural Products Research

(2019) Jörn Piel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining

(2019) Ellis C. O’Neill et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Distinct autocatalytic α-N-methylating precursors expand the borosin RiPP family of peptide natural products

(2019) Marissa R. Quijano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

(2019) Inge Kjærbølling et al.   mSystems

Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal–Bacterial Symbiosis

(2019) Sarah P. Niehs et al.   ACS Chemical Biology

Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria

(2019) Sebastian Schieferdecker et al.   ACS Chemical Biology

A Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human- and Animal-Pathogenic Burkholderia Species

(2019) Felix Trottmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Identification of key enzymes responsible for protolimonoid biosynthesis in plants: Opening the door to azadirachtin production

(2019) Hannah Hodgson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains

(2019) Francisco R. Fields et al.   DRUG DEVELOPMENT RESEARCH

Genome mining- and synthetic biology-enabled production of hypermodified peptides

(2019) Agneya Bhushan et al.   Nature Chemistry

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

(2019) Geoffrey D Hannigan et al.   NUCLEIC ACIDS RESEARCH

Structure elucidation of colibactin and its DNA cross-links

(2019) Mengzhao Xue et al.   SCIENCE

Genomics-Driven Discovery of NO-Donating Diazeniumdiolate Siderophores in Diverse Plant-Associated Bacteria

(2019) Ron Hermenau et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A computational framework to explore large-scale biosynthetic diversity

(2019) Jorge C. Navarro-Muñoz et al.   Nature Chemical Biology

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

(2019) Yuki Sugimoto et al.   SCIENCE

NeuRiPP: Neural network identification of RiPP precursor peptides

(2019) Emmanuel L. C. de los Santos   Scientific Reports

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products

(2019) Nishanth J. Merwin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

(2019) Liu Cao et al.   Cell Systems

Biosynthesis, Synthesis, and Activities of Barnesin A, a NRPS-PKS Hybrid Produced by an Anaerobic Epsilonproteobacterium

(2018) Maja Rischer et al.   ACS Chemical Biology

Genome-based identification of a plant-associated marine bacterium as a rich natural product source

(2018) Reiko Ueoka et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

RiPP antibiotics: biosynthesis and engineering potential

(2018) Graham A Hudson et al.   CURRENT OPINION IN MICROBIOLOGY

Direct Pathway Cloning (DiPaC) to unlock natural product biosynthetic potential

(2018) Christian Greunke et al.   METABOLIC ENGINEERING

Natural products from thioester reductase containing biosynthetic pathways

(2018) Michael W. Mullowney et al.   NATURAL PRODUCT REPORTS

Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species

(2018) Xue Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria

(2018) Fabian Panter et al.   Chemical Science

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome

(2018) Eric J. N. Helfrich et al.   Nature Microbiology

An Optimized Synthetic-Bioinformatic Natural Product Antibiotic Sterilizes Multidrug-Resistant Acinetobacter baumannii-Infected Wounds

(2018) Xavier Vila-Farres et al.   mSphere

Discovery of an Antibacterial Isoindolinone-Containing Tetracyclic Polyketide by Cryptic Gene Activation and Characterization of Its Biosynthetic Gene Cluster

(2018) Wei Li Thong et al.   ACS Chemical Biology

Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria

(2018) Kyle Dunbar et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genomics-Driven Discovery of a Symbiont-Specific Cyclopeptide from Bacteria Residing in the Rice Seedling Blight Fungus

(2018) Sarah Niehs et al.   CHEMBIOCHEM

Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action

(2018) Yan Yan et al.   NATURE

Gramibactin is a bacterial siderophore with a diazeniumdiolate ligand system

(2018) Ron Hermenau et al.   Nature Chemical Biology

Genomics-driven discovery of a linear lipopeptide promoting host colonization by endofungal bacteria

(2018) Sarah P. Niehs et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines

(2018) Claire Pancrace et al.   ACS Chemical Biology

Natural products from anaerobes

(2018) Jeffrey S. Li et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Gene-guided discovery and engineering of branched cyclic peptides in plants

(2018) Roland D. Kersten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atolypenes, Tricyclic Bacterial Sesterterpenes Discovered Using a Multiplexed In Vitro Cas9-TAR Gene Cluster Refactoring Approach

(2018) Seong-Hwan Kim et al.   ACS Synthetic Biology

Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites

(2018) Juliane Fischer et al.   eLife

Characterization of the secondary metabolite biosynthetic gene clusters in archaea

(2018) Shengqin Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Using natural products for drug discovery: the impact of the genomics era

(2017) Mingzi M Zhang et al.   Expert Opinion on Drug Discovery

Function-related replacement of bacterial siderophore pathways

(2017) Hilke Bruns et al.   ISME Journal

Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters

(2017) Xavier Vila-Farres et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discovery of a Cryptic Antifungal Compound from Streptomyces albus J1074 Using High-Throughput Elicitor Screens

(2017) Fei Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Symbiosis-inspired approaches to antibiotic discovery

(2017) Navid Adnani et al.   NATURAL PRODUCT REPORTS

Autocatalytic backbone N-methylation in a family of ribosomal peptide natural products

(2017) Niels S van der Velden et al.   Nature Chemical Biology

CRISPR–Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters

(2017) Mingzi M Zhang et al.   Nature Chemical Biology

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges

(2017) Vinayak Agarwal et al.   Nature Chemical Biology

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery

(2017) Mohammad Alanjary et al.   NUCLEIC ACIDS RESEARCH

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

(2017) Gregory C. A. Amos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution

(2017) Ancheng C. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of the leinamycin family of natural products by mining actinobacterial genomes

(2017) Guohui Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation

(2017) Nicolaus A. Herman et al.   Nature Communications

Astellifadiene: Structure Determination by NMR Spectroscopy and Crystalline Sponge Method, and Elucidation of its Biosynthesis

(2016) Yudai Matsuda et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Discovery of a Mosaic-Like Biosynthetic Assembly Line with a Decarboxylative Off-Loading Mechanism through a Combination of Genome Mining and Imaging

(2016) Mahsa Mir Mohseni et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Direct Capture Technologies for Genomics-Guided Discovery of Natural Products

(2016) Andrew N. Chan et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Computational strategies for genome-based natural product discovery and engineering in fungi

(2016) Theo A.J. van der Lee et al.   FUNGAL GENETICS AND BIOLOGY

Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes

(2016) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Insights into microbial cryptic gene activation and strain improvement: principle, application and technical aspects

(2016) Kozo Ochi   JOURNAL OF ANTIBIOTICS

Natural product discovery: past, present, and future

(2016) Leonard Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Insights into the chemical logic and enzymatic machinery of NRPS assembly lines

(2016) Christopher T. Walsh   NATURAL PRODUCT REPORTS

Human commensals producing a novel antibiotic impair pathogen colonization

(2016) Alexander Zipperer et al.   NATURE

A hybrid polyketide–nonribosomal peptide in nematodes that promotes larval survival

(2016) Qingyao Shou et al.   Nature Chemical Biology

Assembly and clustering of natural antibiotics guides target identification

(2016) Chad W Johnston et al.   Nature Chemical Biology

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

(2016) John Chu et al.   Nature Chemical Biology

Plant metabolic clusters - from genetics to genomics

(2016) Hans-Wilhelm Nützmann et al.   NEW PHYTOLOGIST

Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae

(2016) Xinlu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

(2016) Michael A. Skinnider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed CRISPR/Cas9- and TAR-Mediated Promoter Engineering of Natural Product Biosynthetic Gene Clusters in Yeast

(2016) Hahk-Soo Kang et al.   ACS Synthetic Biology

Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining

(2015) Xiaoyu Tang et al.   ACS Chemical Biology

Bacterial Genome Mining of Enzymatic Tools for Alkyne Biosynthesis

(2015) Xuejun Zhu et al.   ACS Chemical Biology

Epigenetic Genome Mining of an Endophytic Fungus Leads to the Pleiotropic Biosynthesis of Natural Products

(2015) Xu-Ming Mao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery

(2015) Jeffrey D. Rudolf et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection

(2015) Fang Guo et al.   METABOLIC ENGINEERING

Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors

(2015) Jeremy G. Owen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory

(2015) G. Shabuer et al.   SCIENCE

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

(2015) Wenjun Jiang et al.   Nature Communications

Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea

(2015) James C. Charlesworth et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

De novo synthesis of a sunscreen compound in vertebrates

(2015) Andrew R Osborn et al.   eLife

Terpenoid Biosynthesis Off the Beaten Track: Unconventional Cyclases and Their Impact on Biomimetic Synthesis

(2014) Martin Baunach et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

(2014) Hosein Mohimani et al.   JOURNAL OF NATURAL PRODUCTS

A roadmap for natural product discovery based on large-scale genomics and metabolomics

(2014) James R Doroghazi et al.   Nature Chemical Biology

High-throughput platform for the discovery of elicitors of silent bacterial gene clusters

(2014) M. R. Seyedsayamdost   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes

(2014) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products

(2014) Marnix H. Medema et al.   PLoS Computational Biology

Genomics-Driven Discovery of Burkholderic Acid, a Noncanonical, Cryptic Polyketide from Human PathogenicBurkholderiaSpecies

(2012) Jakob Franke et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Malleilactone, a Polyketide Synthase-Derived Virulence Factor Encoded by the Cryptic Secondary Metabolome of Burkholderia pseudomallei Group Pathogens

(2012) John B. Biggins et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A genomic approach to the cryptic secondary metabolome of the anaerobic world

(2012) Anne-Catrin Letzel et al.   NATURAL PRODUCT REPORTS

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

Molecular mechanisms of antibiotic resistance

(2011) Gerard D. Wright   CHEMICAL COMMUNICATIONS

Closthioamide: An Unprecedented Polythioamide Antibiotic from the Strictly Anaerobic Bacterium Clostridium cellulolyticum

(2010) Thorger Lincke et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Biosynthetic Logic of Polyketide Diversity

(2009) Christian Hertweck   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12

(2009) Takeshi Hosaka et al.   NATURE BIOTECHNOLOGY

Triggering cryptic natural product biosynthesis in microorganisms

(2009) Kirstin Scherlach et al.   ORGANIC & BIOMOLECULAR CHEMISTRY