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

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

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

(2016) Natalay Kouprina et al.   CHROMOSOMA

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

(2016) Omar O. Abudayyeh et al.   SCIENCE

A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis

(2016) W. Tao et al.   Chemical Science

Toward Infection-Resistant Surfaces: Achieving High Antimicrobial Peptide Potency by Modulating the Functionality of Polymer Brush and Peptide

(2015) Kai Yu et al.   ACS Applied Materials & Interfaces

Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system

(2015) Hu Zeng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Developing Streptomyces venezuelae as a cell factory for the production of small molecules used in drug discovery

(2015) Eun Ji Kim et al.   ARCHIVES OF PHARMACAL RESEARCH

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Small Molecules Enhance CRISPR Genome Editing in Pluripotent Stem Cells

(2015) Chen Yu et al.   Cell Stem Cell

Genome editing by natural genetic transformation in Streptococcus mutans

(2015) D.A. Morrison et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB- co -4HB) biosynthesis

(2015) Li Lv et al.   METABOLIC ENGINEERING

Regulation of DNA phosphorothioate modifications by the transcriptional regulator DptB inSalmonella

(2015) Qiuxiang Cheng et al.   MOLECULAR MICROBIOLOGY

Metabolic coupling of two small-molecule thiols programs the biosynthesis of lincomycin A

(2015) Qunfei Zhao et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

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

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria

(2015) Ido Yosef 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

Gene silencing by CRISPR interference in mycobacteria

(2015) Eira Choudhary et al.   Nature Communications

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

(2015) Yongxin Li et al.   Scientific Reports

Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB

(2015) Wei He et al.   Scientific Reports

Engineering Translational Activators with CRISPR-Cas System

(2015) Pei Du et al.   ACS Synthetic Biology

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

The Legacy of Nat Sternberg: The Genesis of Cre-loxTechnology

(2015) Michael Yarmolinsky et al.   Annual Review of Virology

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

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

(2014) Bailey Bonet et al.   JOURNAL OF NATURAL PRODUCTS

Pathological phenotypes andin vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system inSalmonella

(2014) Bo Cao et al.   MOLECULAR MICROBIOLOGY

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development

(2014) Chris J. Paddon et al.   NATURE REVIEWS MICROBIOLOGY

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae

(2014) Yulia Yuzenkova et al.   NUCLEIC ACIDS RESEARCH

In Vivo Mutational Characterization of DndE Involved in DNA Phosphorothioate Modification

(2014) Chongde Lai 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

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

(2014) A. A. Gomaa et al.   mBio

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

(2014) Bo Cao et al.   Nature Communications

DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks

(2014) Rui Gan et al.   Scientific Reports

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

(2014) Weiyue Ji 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

Recombinant protein expression in Escherichia coli: advances and challenges

(2014) Germán L. Rosano et al.   Frontiers in Microbiology

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

(2014) Carlos Olano et al.   Microbial Biotechnology

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites

(2013) Kyu-Sang Hwang et al.   BIOTECHNOLOGY ADVANCES

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Incentives for developing new antibiotics or antimicrobial strategies

(2013) U. R. Dahle et al.   BMJ-British Medical Journal

Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

(2012) Wei Hu et al.   CELL RESEARCH

Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity

(2012) Jing Zhang et al.   MOLECULAR CELL

Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs

(2012) Caryn R. Hale et al.   MOLECULAR CELL

RNA processing enables predictable programming of gene expression

(2012) Lei Qi et al.   NATURE BIOTECHNOLOGY

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

(2012) Jun Fu et al.   NATURE BIOTECHNOLOGY

Phosphorothioate DNA as an antioxidant in bacteria

(2012) Xinqiang Xie et al.   NUCLEIC ACIDS RESEARCH

A Novel Target of IscS in Escherichia coli: Participating in DNA Phosphorothioation

(2012) Xianhui An et al.   PLoS One

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes

(2011) Sinan Al-Attar et al.   BIOLOGICAL CHEMISTRY

Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome

(2011) Yumi Iwadate et al.   FEMS MICROBIOLOGY LETTERS

Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion

(2011) T. J. O'Connor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA phosphorothioation is widespread and quantized in bacterial genomes

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

Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site

(2011) A. Hatoum-Aslan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

(2011) B. Wiedenheft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cloning large natural product gene clusters from the environment: Piecing environmental DNA gene clusters back together with TAR

(2010) Jeffrey H. Kim et al.   BIOPOLYMERS

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella

(2010) Tiegang Xu 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

Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

(2010) Rachel E. Haurwitz et al.   SCIENCE

Twenty years hunting for sulfur in DNA

(2010) Shi Chen et al.   Protein & Cell

Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters

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

Tailoring the P450 Monooxygenase Gene for FR-008/Candicidin Biosynthesis

(2009) S. Chen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic engineering of Streptomyces venezuelae for malonyl-CoA biosynthesis to enhance heterologous production of polyketides

(2009) Sushila Maharjan et al.   BIOTECHNOLOGY LETTERS

DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus

(2009) Tiegang Xu et al.   BMC MICROBIOLOGY

Biosynthesis of Actinorhodin and Related Antibiotics: Discovery of Alternative Routes for Quinone Formation Encoded in the act Gene Cluster

(2009) Susumu Okamoto et al.   CHEMISTRY & BIOLOGY

Functional analysis ofspfDgene involved in DNA phosphorothioation inPseudomonas fluorescensPf0-1

(2009) Fen Yao et al.   FEBS LETTERS

Incomplete β-Ketone Processing as a Mechanism for Polyene Structural Variation in the FR-008/Candicidin Complex

(2008) Yongjun Zhou et al.   CHEMISTRY & BIOLOGY

Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis

(2008) T. Morimoto et al.   DNA RESEARCH

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

(2008) J. Carte et al.   GENES & DEVELOPMENT

Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins inSalmonella enterica

(2008) J. Christian Perez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic remodeling of the fungal secondary metabolome

(2008) Russell B. Williams et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

A chemical epigenetics approach for engineering the in situbiosynthesis of a cryptic natural product from Aspergillus niger

(2008) Jon C. Henrikson et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE