Heterologous expression-facilitated natural products’ discovery in actinomycetes

Genome engineering for microbial natural product discovery

(2018) Si-Sun Choi et al.   CURRENT OPINION IN MICROBIOLOGY

Streptomyces species: Ideal chassis for natural product discovery and overproduction

(2018) Ran Liu et al.   METABOLIC ENGINEERING

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

(2018) Christian Greunke et al.   METABOLIC ENGINEERING

Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters

(2018) Dimitris Kallifidas et al.   Microbial Cell Factories

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Discovery, Biosynthesis, and Heterologous Production of Streptoseomycin, an Anti-Microaerophilic Bacteria Macrodilactone

(2018) Bo Zhang et al.   ORGANIC LETTERS

Genomics-Driven Natural Product Discovery in Actinomycetes

(2018) Guoqing Niu   TRENDS IN BIOTECHNOLOGY

Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens

(2018) Bradley M. Hover et al.   Nature Microbiology

HEx: A heterologous expression platform for the discovery of fungal natural products

(2018) Colin J. B. Harvey et al.   Science Advances

Biosynthesis of Tropolones in Streptomyces spp.: Interweaving Biosynthesis and Degradation of Phenylacetic Acid and Hydroxylations on the Tropone Ring

(2018) Xuefei Chen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR-Cpf1-Assisted Multiplex Genome Editing and Transcriptional Repression in Streptomyces

(2018) Lei Li et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters

(2018) Maksym Myronovskyi et al.   METABOLIC ENGINEERING

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

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

Activation and mechanism of a cryptic oviedomycin gene cluster via the disruption of a global regulatory gene,adpA, inStreptomyces ansochromogenes

(2017) Jingjing Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PCR-Independent Method of Transformation-Associated Recombination Reveals the Cosmomycin Biosynthetic Gene Cluster in an Ocean Streptomycete

(2017) Charles B. Larson et al.   JOURNAL OF NATURAL PRODUCTS

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

Heterologous expression of pikromycin biosynthetic gene cluster using Streptomyces artificial chromosome system

(2017) Hye-rim Pyeon et al.   Microbial Cell Factories

Actinomycetes: still a source of novel antibiotics

(2017) Olga Genilloud   NATURAL PRODUCT REPORTS

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

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

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

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

ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes

(2017) Hailong Wang 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

Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species

(2017) Hee-Ju Nah et al.   Frontiers in Microbiology

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

(2016) Min Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe

(2016) Paul C. M. Fogg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Discovery of Unusual Biaryl Polyketides by Activation of a SilentStreptomyces venezuelaeBiosynthetic Gene Cluster

(2016) Anyarat Thanapipatsiri et al.   CHEMBIOCHEM

Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology

(2016) Natalay Kouprina et al.   CHROMOSOMA

Gifted microbes for genome mining and natural product discovery

(2016) Richard H. Baltz   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

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

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

The evolution of genome mining in microbes – a review

(2016) Nadine Ziemert et al.   NATURAL PRODUCT REPORTS

Engineering microbial hosts for production of bacterial natural products

(2016) Mingzi M. Zhang et al.   NATURAL PRODUCT REPORTS

Native and engineered promoters in natural product discovery

(2016) Maksym Myronovskyi et al.   NATURAL PRODUCT REPORTS

New tools for reconstruction and heterologous expression of natural product biosynthetic gene clusters

(2016) Yunzi Luo et al.   NATURAL PRODUCT REPORTS

Targeted isolation and cloning of 100-kb microbial genomic sequences by Cas9-assisted targeting of chromosome segments

(2016) Wenjun Jiang et al.   Nature Protocols

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Hybrubins: Bipyrrole Tetramic Acids Obtained by Crosstalk between a Truncated Undecylprodigiosin Pathway and Heterologous Tetramic Acid Biosynthetic Genes

(2016) Zhilong Zhao et al.   ORGANIC LETTERS

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

Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts

(2016) Weishan Wang et al.   ACS Synthetic Biology

How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity

(2016) Grace Yim et al.   ACS Infectious Diseases

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

(2015) Xiaoyu Tang et al.   ACS Chemical Biology

Engineered biosynthesis of natural products in heterologous hosts

(2015) Yunzi Luo et al.   CHEMICAL SOCIETY REVIEWS

Iterative Mechanism of Macrodiolide Formation in the Anticancer Compound Conglobatin

(2015) Yongjun Zhou et al.   CHEMISTRY & BIOLOGY

Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes

(2015) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Culture-independent discovery of natural products from soil metagenomes

(2015) Micah Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

A stepwise increase in pristinamycin II biosynthesis by Streptomyces pristinaespiralis through combinatorial metabolic engineering

(2015) Lei Li et al.   METABOLIC ENGINEERING

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

(2015) Peter J. Rutledge et al.   NATURE REVIEWS MICROBIOLOGY

Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast

(2015) Nicholas C.O. Lee et al.   NUCLEIC ACIDS RESEARCH

Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products inStreptomyces

(2015) Chaoxian Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Wenjun Jiang et al.   Nature Communications

Genome engineering and direct cloning of antibiotic gene clusters via phage ϕBT1 integrase-mediated site-specific recombination in Streptomyces

(2015) Deyao Du et al.   Scientific Reports

Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2)

(2015) Jia Yin et al.   Scientific Reports

Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis

(2015) Yongxin Li et al.   Scientific Reports

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

A novel Streptomyces spp. integration vector derived from the S. venezuelae phage, SV1

(2014) Bahgat Fayed et al.   BMC BIOTECHNOLOGY

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

(2014) Peter Cimermancic et al.   CELL

Recent advances in natural product discovery

(2014) Yunzi Luo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Direct Capture and Heterologous Expression of Salinispora Natural Product Genes for the Biosynthesis of Enterocin

(2014) Bailey Bonet 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

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

Targeted Capture and Heterologous Expression of the Pseudoalteromonas Alterochromide Gene Cluster in Escherichia coli Represents a Promising Natural Product Exploratory Platform

(2014) Avena C. Ross et al.   ACS Synthetic Biology

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

Activation and identification of five clusters for secondary metabolites inStreptomyces albus J1074

(2014) Carlos Olano et al.   Microbial Biotechnology

Arimetamycin A: Improving Clinically Relevant Families of Natural Products through Sequence-Guided Screening of Soil Metagenomes

(2013) Hahk-Soo Kang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An Engineered Strong Promoter for Streptomycetes

(2013) W. Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways

(2013) Gregory L. Challis   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

(2013) Brian O. Bachmann et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Phage P1-Derived Artificial Chromosomes Facilitate Heterologous Expression of the FK506 Gene Cluster

(2013) Adam C. Jones et al.   PLoS One

Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening

(2013) F.-Y. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products

(2013) J. G. Owen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster

(2013) John D. Sidda et al.   Chemical Science

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

(2013) Yunzi Luo et al.   Nature Communications

Engineered Streptomyces avermitilis Host for Heterologous Expression of Biosynthetic Gene Cluster for Secondary Metabolites

(2013) Mamoru Komatsu et al.   ACS Synthetic Biology

High-Throughput Screening for Streptomyces Antibiotic Biosynthesis Activators

(2012) Li Chen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tetarimycin A, an MRSA-Active Antibiotic Identified through Induced Expression of Environmental DNA Gene Clusters

(2012) Dimitris Kallifidas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting

(2012) Jun Fu et al.   NATURE BIOTECHNOLOGY

ThioFinder: A Web-Based Tool for the Identification of Thiopeptide Gene Clusters in DNA Sequences

(2012) Jing Li et al.   PLoS One

Streptomyces autolyticus JX-47 Large-Insert Bacterial Artificial Chromosome Library Construction and Identification of Clones Covering Geldanamycin Biosynthesis Gene Cluster

(2011) Shikun Dai et al.   CURRENT MICROBIOLOGY

Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms)

(2011) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler

(2011) Zengyi Shao et al.   Molecular BioSystems

A system for the targeted amplification of bacterial gene clusters multiplies antibiotic yield in Streptomyces coelicolor

(2011) T. Murakami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens

(2011) L. Laureti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism

(2010) M. Komatsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Cleavage is Independent of Synapsis during Streptomyces Phage φBT1 Integrase-Mediated Site-Specific Recombination

(2010) Lin Zhang et al.   Journal of Molecular Cell Biology

Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters

(2010) Juan Pablo Gomez-Escribano et al.   Microbial Biotechnology

Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis

(2010) Yvonne Mast et al.   Microbial Biotechnology

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

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Functional expression of the Cre recombinase in actinomycetes

(2008) Marta Fedoryshyn et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The Mildiomycin Biosynthesis: Initial Steps for Sequential Generation of 5-Hydroxymethylcytidine 5′-Monophosphate and 5-Hydroxymethylcytosine inStreptoverticillium rimofaciensZJU5119

(2008) Li Li et al.   CHEMBIOCHEM

Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae

(2008) Natalay Kouprina et al.   Nature Protocols

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

(2008) Zengyi Shao et al.   NUCLEIC ACIDS RESEARCH