The Design-Build-Test-Learn cycle for metabolic engineering of Streptomycetes

A Streptomyces venezuelae Cell-Free Toolkit for Synthetic Biology

(2021) Simon J. Moore et al.   ACS Synthetic Biology

Statistical Design of Experiments for Synthetic Biology

(2021) James Gilman et al.   ACS Synthetic Biology

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

(2021) Satria A Kautsar et al.   GigaScience

Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination

(2021) Behnam Enghiad et al.   Nature Communications

Multiomics Data Collection, Visualization, and Utilization for Guiding Metabolic Engineering

(2021) Somtirtha Roy et al.   Frontiers in Bioengineering and Biotechnology

Transcription factor-based biosensors: a molecular-guided approach for natural product engineering

(2021) Melissa M Mitchler et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering of Streptomyces lividans for heterologous expression of secondary metabolite gene clusters

(2020) Yousra Ahmed et al.   Microbial Cell Factories

Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation

(2020) Zheren Zhang et al.   Science Advances

The Science of Antibiotic Discovery

(2020) Kim Lewis   CELL

Fine-tuning the regulation of Cas9 expression levels for efficient CRISPR-Cas9 mediated recombination in Streptomyces

(2020) Suhui Ye et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks

(2020) Archana Hari et al.   NUCLEIC ACIDS RESEARCH

Review on natural products databases: where to find data in 2020

(2020) Maria Sorokina et al.   Journal of Cheminformatics

Transcriptome and translatome profiles of Streptomyces species in different growth phases

(2020) Woori Kim et al.   Scientific Data

System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces

(2020) Yongjae Lee et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes

(2020) Yaojun Tong et al.   Nature Protocols

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

(2020) Zhenquan Lin et al.   Frontiers in Bioengineering and Biotechnology

An Update on Molecular Tools for Genetic Engineering of Actinomycetes—The Source of Important Antibiotics and Other Valuable Compounds

(2020) Lena Mitousis et al.   Antibiotics-Basel

BiG-FAM: the biosynthetic gene cluster families database

(2020) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

StreptomeDB 3.0: an updated compendium of streptomycetes natural products

(2020) Aurélien F A Moumbock et al.   NUCLEIC ACIDS RESEARCH

Cryptic or Silent? The Known Unknowns, Unknown Knowns, and Unknown Unknowns of Secondary Metabolism

(2020) Paul A. Hoskisson et al.   mBio

A machine learning Automated Recommendation Tool for synthetic biology

(2020) Tijana Radivojević et al.   Nature Communications

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

(2020) Jie Zhang et al.   Nature Communications

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences

(2020) Michael A. Skinnider et al.   Nature Communications

Automating Cloning by Natural Transformation

(2020) Xinglin Jiang et al.   ACS Synthetic Biology

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

(2020) Yongjae Lee et al.   Scientific Data

Synthetic Inducible Regulatory Systems Optimized for the Modulation of Secondary Metabolite Production in Streptomyces

(2019) Chang-Hun Ji et al.   ACS Synthetic Biology

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

(2019) Kai Dührkop et al.   NATURE METHODS

CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

(2019) Oriol Senan et al.   BIOINFORMATICS

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning

(2019) Paul Opgenorth et al.   ACS Synthetic Biology

Building a global alliance of biofoundries

(2019) Nathan Hillson et al.   Nature Communications

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

(2019) Yaojun Tong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcription Unit Architecture of Streptomyces lividans TK24

(2019) Yongjae Lee et al.   Frontiers in Microbiology

Construction of a new integrating vector from actinophage ϕOZJ and its use in multiplex Streptomyces transformation

(2019) Bryan Ko et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

A computational framework to explore large-scale biosynthetic diversity

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

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase

(2019) Krishnaveni Palaniappan et al.   NUCLEIC ACIDS RESEARCH

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery

(2019) Jeffrey A. van Santen et al.   ACS Central Science

Expanding the palette of Streptomyces -based cell-free protein synthesis systems with enhanced yields

(2018) Jian Li et al.   BIOCHEMICAL ENGINEERING JOURNAL

An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies

(2018) León Toro et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Modelling the metabolism of protein secretion through the Tat route in Streptomyces lividans

(2018) José R. Valverde et al.   BMC MICROBIOLOGY

Metabolomics tools for the synthetic biology of natural products

(2018) Katherine A Hollywood et al.   CURRENT OPINION IN BIOTECHNOLOGY

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

(2018) Emilia Palazzotto et al.   CURRENT OPINION IN MICROBIOLOGY

Design, development and application of whole-cell based antibiotic-specific biosensor

(2018) Yuriy Rebets et al.   METABOLIC ENGINEERING

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

(2018) Christian Greunke et al.   METABOLIC ENGINEERING

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

(2018) Baudoin Delépine et al.   METABOLIC ENGINEERING

Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces

(2018) Adelfia Talà 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

De novo DNA synthesis using polymerase-nucleotide conjugates

(2018) Sebastian Palluk et al.   NATURE BIOTECHNOLOGY

A set of synthetic versatile genetic control elements for the efficient expression of genes in Actinobacteria

(2018) Lilya Horbal et al.   Scientific Reports

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

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

Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

(2018) Omkar S. Mohite et al.   Biotechnology Journal

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

(2018) Maksym Myronovskyi et al.   METABOLIC ENGINEERING

Development of a strictly regulated xylose-induced expression system in Streptomyces

(2018) Yuji Noguchi et al.   Microbial Cell Factories

Dereplication of microbial metabolites through database search of mass spectra

(2018) Hosein Mohimani et al.   Nature Communications

Predicting strain engineering strategies using iKS1317: a genome‐scale metabolic model of Streptomyces coelicolor

(2018) Tjaša Kumelj et al.   Biotechnology Journal

A genetics-free method for high-throughput discovery of cryptic microbial metabolites

(2018) Fei Xu et al.   Nature Chemical Biology

Engineered Streptomyces lividans Strains for Optimal Identification and Expression of Cryptic Biosynthetic Gene Clusters

(2018) Qinying Peng et al.   Frontiers in Microbiology

aMSGE: advanced multiplex site-specific genome engineering with orthogonal modular recombinases in actinomycetes

(2018) Lei Li et al.   METABOLIC ENGINEERING

Combining metabolomics and network analysis to improve tacrolimus production in Streptomyces tsukubaensis using different exogenous feedings

(2017) Cheng Wang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Multiplexed site-specific genome engineering for overproducing bioactive secondary metabolites in actinomycetes

(2017) Lei Li et al.   METABOLIC ENGINEERING

Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria

(2017) Gao-Yi Tan et al.   METABOLIC ENGINEERING

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

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

In situ cultivation of previously uncultivable microorganisms using the ichip

(2017) Brittany Berdy et al.   Nature Protocols

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

ClusterCAD: a computational platform for type I modular polyketide synthase design

(2017) Clara H Eng et al.   NUCLEIC ACIDS RESEARCH

Development of a Biosensor Concept to Detect the Production of Cluster-Specific Secondary Metabolites

(2017) Yi-Qian Sun et al.   ACS Synthetic Biology

Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool

(2017) Simon J. Moore et al.   Biotechnology Journal

Streptomyces exploration is triggered by fungal interactions and volatile signals

(2017) Stephanie E Jones et al.   eLife

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

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

Heterologous expression of oxytetracycline biosynthetic gene cluster in Streptomyces venezuelae WVR2006 to improve production level and to alter fermentation process

(2016) Shouliang Yin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2016) Natalay Kouprina et al.   CHROMOSOMA

Natural product discovery: past, present, and future

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

Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

(2016) Pablo Carbonell 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

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

Cloning and Heterologous Expression of the Grecocycline Biosynthetic Gene Cluster

(2016) Oksana Bilyk et al.   PLoS One

Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae

(2016) Ryan M. Phelan et al.   ACS Synthetic Biology

One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces

(2015) He Huang et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

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

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

Taxonomy, Physiology, and Natural Products of Actinobacteria

(2015) Essaid Ait Barka et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

Systematic Identification of a Panel of Strong Constitutive Promoters from Streptomyces albus

(2015) Yunzi Luo et al.   ACS Synthetic Biology

Novel and tightly regulated resorcinol and cumate-inducible expression systems for Streptomyces and other actinobacteria

(2014) Liliya Horbal et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Applications of genome-scale metabolic network model in metabolic engineering

(2014) Byoungjin Kim et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Synthetic Promoter Library for Modulation of Actinorhodin Production in Streptomyces coelicolor A3(2)

(2014) Sujata Vijay Sohoni et al.   PLoS One

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

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

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

An Engineered Strong Promoter for Streptomycetes

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

The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island

(2013) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Heterologous expression of natural product biosynthetic gene clusters in Streptomyces coelicolor: from genome mining to manipulation of biosynthetic pathways

(2013) Juan Pablo Gomez-Escribano et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes

(2013) Theresa Siegl et al.   METABOLIC ENGINEERING

Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

(2013) Di Huang et al.   Microbial Cell Factories

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

(2013) Mamoru Komatsu et al.   ACS Synthetic Biology

Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold

(2013) Zengyi Shao et al.   ACS Synthetic Biology

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

(2012) Jun Fu et al.   NATURE BIOTECHNOLOGY

Exploiting Adaptive Laboratory Evolution of Streptomyces clavuligerus for Antibiotic Discovery and Overproduction

(2012) Pep Charusanti et al.   PLoS One

Combinatorial Biosynthesis of Cyclic Lipopeptide Antibiotics: A Model for Synthetic Biology To Accelerate the Evolution of Secondary Metabolite Biosynthetic Pathways

(2012) Richard H. Baltz   ACS Synthetic Biology

DeviceEditor visual biological CAD canvas

(2012) Joanna Chen et al.   Journal of Biological Engineering

β-Glucuronidase as a Sensitive and Versatile Reporter in Actinomycetes

(2011) Maksym Myronovskyi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

j5 DNA Assembly Design Automation Software

(2011) Nathan J. Hillson et al.   ACS Synthetic Biology

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

(2010) Kay Nieselt et al.   BMC GENOMICS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters

(2010) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

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

Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters

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

Medium optimization for the production of avermectin B1a by Streptomyces avermitilis 14-12A using response surface methodology

(2009) Hong Gao et al.   BIORESOURCE TECHNOLOGY

Rapid Cloning and Heterologous Expression of the Meridamycin Biosynthetic Gene Cluster Using a VersatileEscherichia coli−StreptomycesArtificial Chromosome Vector, pSBAC⊥

(2009) Hongbo Liu et al.   JOURNAL OF NATURAL PRODUCTS