Genome mining as a biotechnological tool for the discovery of novel marine natural products

Automated structure prediction of trans-acyltransferase polyketide synthase products

(2019) Eric J. N. Helfrich et al.   Nature Chemical Biology

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

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

Synthetic Genomics: From DNA Synthesis to Genome Design

(2018) Lianrong Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules

(2018) G. Seghal Kiran et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

(2018) Jun Shang et al.   Journal of Chemical Information and Modeling

Marine natural products

(2018) John W. Blunt et al.   NATURAL PRODUCT REPORTS

Resistance to nonribosomal peptide antibiotics mediated by d-stereospecific peptidases

(2018) Yong-Xin Li et al.   Nature Chemical Biology

Marine Natural Products in Medicinal Chemistry

(2018) Carlos Jiménez   ACS Medicinal Chemistry Letters

Dereplication of microbial metabolites through database search of mass spectra

(2018) Hosein Mohimani et al.   Nature Communications

Producing Novel Fibrinolytic Isoindolinone Derivatives in Marine Fungus Stachybotrys longispora FG216 by the Rational Supply of Amino Compounds According to Its Biosynthesis Pathway

(2017) Ying Yin et al.   Marine Drugs

Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics

(2017) Xuan Zou et al.   MEDICINAL RESEARCH REVIEWS

Releasing the potential power of terpene synthases by a robust precursor supply platform

(2017) Guangkai Bian et al.   METABOLIC ENGINEERING

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

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

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Genome Mining and Activation of a Silent PKS/NRPS Gene Cluster Direct the Production of Totopotensamides

(2017) Ruidong Chen et al.   ORGANIC LETTERS

Evolutionary radiation of lanthipeptides in marine cyanobacteria

(2017) Andres Cubillos-Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genusMoorea

(2017) Tiago Leao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation and characterization of a cryptic gene cluster reveals a cyclization cascade for polycyclic tetramate macrolactams

(2017) Subhasish Saha et al.   Chemical Science

Marine microbiome as source of natural products

(2017) Fernando de la Calle   Microbial Biotechnology

New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18

(2017) Constanze Paulus et al.   Scientific Reports

Production of a Novel Amide-Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster inStreptomycessp. MSC090213JE08

(2016) Danyao Du et al.   CHEMBIOCHEM

Biosynthetic Gene Cluster for Surugamide A Encompasses an Unrelated Decapeptide, Surugamide F

(2016) Akihiro Ninomiya et al.   CHEMBIOCHEM

Advanced tools in marine natural drug discovery

(2016) Guojian Zhang et al.   CURRENT OPINION IN BIOTECHNOLOGY

An analysis of FDA-approved drugs: natural products and their derivatives

(2016) Eric Patridge et al.   DRUG DISCOVERY TODAY

Natural Products as Sources of New Drugs from 1981 to 2014

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

Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

(2016) Juan Gomez-Escribano et al.   Marine Drugs

Synthesis of Bisindole Alkaloids from the Apocynaceae Which Contain a Macroline or Sarpagine Unit: A Review

(2016) Md Rahman et al.   MOLECULES

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

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

Multi-Substrate Terpene Synthases: Their Occurrence and Physiological Significance

(2016) Leila Pazouki et al.   Frontiers in Plant Science

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

(2016) Maria Maansson et al.   mSystems

Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm

(2015) Lian Yang et al.   CHEMISTRY & BIOLOGY

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

Bioactive Polycyclic Tetramate Macrolactams from Lysobacter enzymogenes and Their Absolute Configurations by Theoretical ECD Calculations

(2015) Liangxiong Xu et al.   JOURNAL OF NATURAL PRODUCTS

The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms

(2015) F. Reen et al.   Marine Drugs

Exploring cyanobacterial genomes for natural product biosynthesis pathways

(2015) Melinda L. Micallef et al.   Marine Genomics

Dereplication: racing to speed up the natural products discovery process

(2015) Susana P. Gaudêncio et al.   NATURAL PRODUCT REPORTS

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Molecular Basis for Stellatic Acid Biosynthesis: A Genome Mining Approach for Discovery of Sesterterpene Synthases

(2015) Yudai Matsuda et al.   ORGANIC LETTERS

Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone

(2015) Warren Lau et al.   SCIENCE

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products

(2015) Chad W. Johnston et al.   Nature Communications

Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates

(2015) Marla Trindade et al.   Frontiers in Microbiology

Heterologous Reconstitution of Ikarugamycin Biosynthesis inE. coli

(2014) Janine Antosch et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Mechanistic Insights into Polycycle Formation by Reductive Cyclization in Ikarugamycin Biosynthesis

(2014) Guangtao Zhang 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

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

(2014) Aleksandr Milshteyn et al.   CHEMISTRY & BIOLOGY

The chemical logic of plant natural product biosynthesis

(2014) Gülbenk Anarat-Cappillino et al.   CURRENT OPINION IN PLANT BIOLOGY

Sioxanthin, a novel glycosylated carotenoid, reveals an unusual subclustered biosynthetic pathway

(2014) Taylor K. S. Richter et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of an Orphan Diterpenoid Biosynthetic Operon from Salinispora arenicola

(2014) Meimei Xu et al.   JOURNAL OF NATURAL PRODUCTS

Caryophyllene Sesquiterpenes from the Marine-Derived Fungus Ascotricha sp. ZJ-M-5 by the One Strain–Many Compounds Strategy

(2014) Wen-Jing Wang et al.   JOURNAL OF NATURAL PRODUCTS

Co-Cultivation—A Powerful Emerging Tool for Enhancing the Chemical Diversity of Microorganisms

(2014) Andreas Marmann et al.   Marine Drugs

Mass spectrometry of natural products: current, emerging and future technologies

(2014) Amina Bouslimani et al.   NATURAL PRODUCT REPORTS

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

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

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

(2014) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

(2014) Kazuya Yamanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway

(2014) J. Vestola 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

Discovery of the Antibiotic Phosacetamycin via a New Mass Spectrometry-Based Method for Phosphonic Acid Detection

(2013) Bradley S. Evans et al.   ACS Chemical Biology

Use of a Phosphonate Methyltransferase in the Identification of the Fosfazinomycin Biosynthetic Gene Cluster

(2013) Jiangtao Gao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides

(2013) Niina Leikoski et al.   CHEMISTRY & BIOLOGY

Identification of micromonolactam, a new polyene macrocyclic lactam from two marine Micromonospora strains using chemical and molecular methods: clarification of the biosynthetic pathway from a glutamate starter unit

(2013) Elizabeth Julia Skellam et al.   JOURNAL OF ANTIBIOTICS

Classification of the Adenylation and Acyl-Transferase Activity of NRPS and PKS Systems Using Ensembles of Substrate Specific Hidden Markov Models

(2013) Barzan I. Khayatt et al.   PLoS One

Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster

(2013) Yunzi Luo et al.   Nature Communications

Discovery, Biosynthesis, and Engineering of Lantipeptides

(2012) Patrick J. Knerr et al.   Annual Review of Biochemistry

The bifunctional role of aconitase inStreptomyces viridochromogenesTü494

(2012) Ewelina Michta et al.   ENVIRONMENTAL MICROBIOLOGY

Advances in Aspergillus secondary metabolite research in the post-genomic era

(2012) James F. Sanchez et al.   NATURAL PRODUCT REPORTS

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

(2012) A. Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Natural products: An evolving role in future drug discovery

(2011) Bhuwan B. Mishra et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Exploiting a Global Regulator for Small Molecule Discovery inPhotorhabdus luminescens

(2010) Renee Kontnik et al.   ACS Chemical Biology

The Discovery of Salinosporamide K from the Marine Bacterium “Salinispora pacifica” by Genome Mining Gives Insight into Pathway Evolution

(2010) Alessandra S. Eustáquio et al.   CHEMBIOCHEM

Marine pharmacology in 2007–8: Marine compounds with antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; affecting the immune and nervous system, and other miscellaneous mechanisms of action

(2010) Alejandro M.S. Mayer et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

The expanding role of marine microbes in pharmaceutical development

(2010) Amanda L Waters et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome mining for ribosomally synthesized natural products

(2010) Juan E Velásquez et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NMR methods for unravelling the spectra of complex mixtures

(2010) Ramon Novoa-Carballal et al.   NATURAL PRODUCT REPORTS

Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria

(2010) J. A. V. Blodgett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria

(2010) B. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small-molecule elicitation of microbial secondary metabolites

(2010) Robin K. Pettit   Microbial Biotechnology

Highly Diverse Cyanobactins in Strains of the Genus Anabaena

(2009) N. Leikoski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Strategies for the Discovery of New Natural Products by Genome Mining

(2009) Malek Zerikly et al.   CHEMBIOCHEM

Genomic basis for natural product biosynthetic diversity in the actinomycetes

(2009) Markus Nett et al.   NATURAL PRODUCT REPORTS

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

(2009) Takeshi Hosaka et al.   NATURE BIOTECHNOLOGY

Dereplication and de novo sequencing of nonribosomal peptides

(2009) Julio Ng et al.   NATURE METHODS

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

Microcyclamide Biosynthesis in Two Strains of Microcystis aeruginosa: from Structure to Genes and Vice Versa

(2008) N. Ziemert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Widespread Occurrence and Lateral Transfer of the Cyanobactin Biosynthesis Gene Cluster in Cyanobacteria

(2008) N. Leikoski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation of Aerucyclamides C and D and Structure Revision of Microcyclamide 7806A: Heterocyclic Ribosomal Peptides fromMicrocystis aeruginosaPCC 7806 and Their Antiparasite Evaluation

(2008) Cyril Portmann et al.   JOURNAL OF NATURAL PRODUCTS

Drug development from marine natural products

(2008) Tadeusz F. Molinski et al.   NATURE REVIEWS DRUG DISCOVERY