Applications of CRISPR/Cas System to Bacterial Metabolic Engineering

CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog

(2018) Ganesh V. Pusapati et al.   DEVELOPMENTAL CELL

A Robust CRISPR Interference Gene Repression System in Pseudomonas

(2018) Sue Zanne Tan et al.   JOURNAL OF BACTERIOLOGY

RNA-guided single/double gene repressions in Corynebacterium glutamicum using an efficient CRISPR interference and its application to industrial strain

(2018) Jaehyun Park et al.   Microbial Cell Factories

CRISPR-Cas9-based genome-wide screening of Toxoplasma gondii

(2018) Saima M Sidik et al.   Nature Protocols

One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains

(2018) Jung Eun Yang et al.   Nature Communications

High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli

(2018) Suhyung Cho et al.   ACS Synthetic Biology

Development of an Efficient Genome Editing Tool in Bacillus licheniformis Using CRISPR-Cas9 Nickase

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

Investigating CRISPR-Cas systems in Clostridium botulinum via bioinformatics tools

(2017) Manica Negahdaripour et al.   INFECTION GENETICS AND EVOLUTION

Efficient de novo synthesis of resveratrol by metabolically engineered Escherichia coli

(2017) Junjun Wu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

A two-plasmid inducible CRISPR/Cas9 genome editing tool for Clostridium acetobutylicum

(2017) François Wasels et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Rapid and Efficient Genome Editing in Staphylococcus aureus by Using an Engineered CRISPR/Cas9 System

(2017) Weizhong Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway

(2017) Xinna Zhu et al.   METABOLIC ENGINEERING

CRISPR/Cas9-coupled recombineering for metabolic engineering of Corynebacterium glutamicum

(2017) Jae Sung Cho et al.   METABOLIC ENGINEERING

CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli

(2017) Seong Keun Kim et al.   Microbial Cell Factories

CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production

(2017) Brady F. Cress et al.   Microbial Cell Factories

Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum

(2017) Jiao Liu et al.   Microbial Cell Factories

Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system

(2017) Feng Peng et al.   Microbial Cell Factories

Development of a CRISPR/Cas9-mediated gene-editing tool in Streptomyces rimosus

(2017) Haiyan Jia et al.   MICROBIOLOGY-SGM

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

(2017) Fadi J Najm et al.   NATURE BIOTECHNOLOGY

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

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

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

Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

(2017) Lindsey A Lonowski et al.   Nature Protocols

Botulinum Neurotoxins: Biology, Pharmacology, and Toxicology

(2017) Marco Pirazzini et al.   PHARMACOLOGICAL REVIEWS

Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization

(2017) Serif Senturk et al.   Nature Communications

Programmable DNA looping using engineered bivalent dCas9 complexes

(2017) Nan Hao et al.   Nature Communications

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

(2017) Ioannis Mougiakos et al.   Nature Communications

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

(2017) Aude Bernheim et al.   Nature Communications

CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum

(2017) Yu Jiang et al.   Nature Communications

sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity

(2017) Raj Chari et al.   ACS Synthetic Biology

Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis

(2017) Meng-Ying Wu et al.   ACS Synthetic Biology

Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9

(2017) Ioannis Mougiakos et al.   ACS Synthetic Biology

Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis

(2017) Kinga Umenhoffer et al.   ACS Synthetic Biology

Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform

(2017) Jeremy M. Rock et al.   Nature Microbiology

Chromosomal Targeting by the Type III-A CRISPR-Cas System Can Reshape Genomes in Staphylococcus aureus

(2017) Jing Guan et al.   mSphere

Correction: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool

(2017) Manuel Stemmer et al.   PLoS One

Rational modular design of metabolic network for efficient production of plant polyphenol pinosylvin

(2017) Junjun Wu et al.   Scientific Reports

Using CRISPR-Cas9-mediated genome editing to generate C. difficile mutants defective in selenoproteins synthesis

(2017) Kathleen N. McAllister et al.   Scientific Reports

CRISPR/Cas9 in Genome Editing and Beyond

(2016) Haifeng Wang et al.   Annual Review of Biochemistry

Editing of the Bacillus subtilis Genome by the CRISPR-Cas9 System

(2016) Josef Altenbuchner   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene transcription repression inClostridium beijerinckiiusing CRISPR-dCas9

(2016) Yi Wang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome editing of Clostridium autoethanogenum using CRISPR/Cas9

(2016) Shilpa Nagaraju et al.   Biotechnology for Biofuels

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

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

(2016) Jason M. Peters et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Natural polyphenols: potential in the prevention of sexually transmitted viral infections

(2016) Abhijit A. Date et al.   DRUG DISCOVERY TODAY

In vitro antileishmanial activity of trans-stilbene and terphenyl compounds

(2016) Germano Castelli et al.   EXPERIMENTAL PARASITOLOGY

CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production

(2016) Seong Keun Kim et al.   METABOLIC ENGINEERING

Enhanced protein and biochemical production using CRISPRi-based growth switches

(2016) Songyuan Li et al.   METABOLIC ENGINEERING

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

(2016) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

Investigating essential gene function inMycobacterium tuberculosisusing an efficient CRISPR interference system

(2016) Atul K. Singh et al.   NUCLEIC ACIDS RESEARCH

A novel process for obtaining pinosylvin using combinatorial bioengineering in Escherichia coli

(2016) Jing-long Liang et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable “Clean” Mutant Selection in Clostridium beijerinckii as an Example

(2016) Yi Wang et al.   ACS Synthetic Biology

Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi)

(2016) Sara Cleto et al.   ACS Synthetic Biology

Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli

(2016) Min-Ji Heo et al.   ACS Synthetic Biology

Clostridium difficile Toxins A and B: Insights into Pathogenic Properties and Extraintestinal Effects

(2016) Stefano Di Bella et al.   Toxins

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

An Active Type I-E CRISPR-Cas System Identified in Streptomyces avermitilis

(2016) Yi Qiu et al.   PLoS One

Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium

(2016) Michael E. Pyne et al.   Scientific Reports

tCRISPRi: tunable and reversible, one-step control of gene expression

(2016) Xin-tian Li et al.   Scientific Reports

Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products

(2015) Judith Becker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.

(2015) Honglei Liu et al.   BIOINFORMATICS

WGE: a CRISPR database for genome engineering: Fig. 1.

(2015) Alex Hodgkins et al.   BIOINFORMATICS

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system

(2015) Yi Wang et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing

(2015) Yifan Li et al.   METABOLIC ENGINEERING

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

Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri

(2015)   MICROBIOLOGY-SGM

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

(2015) Silvana Konermann et al.   NATURE

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

(2015) Miguel A Moreno-Mateos et al.   NATURE METHODS

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli

(2015) Junjun Wu et al.   Scientific Reports

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

Discovery of Clostrubin, an Exceptional Polyphenolic Polyketide Antibiotic from a Strictly Anaerobic Bacterium

(2014) Sacha Pidot et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool

(2014) Carlotta Ronda et al.   BIOTECHNOLOGY AND BIOENGINEERING

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives

(2014) Franca Rossi et al.   FOOD MICROBIOLOGY

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

(2014) Michelle L. Luo et al.   NUCLEIC ACIDS RESEARCH

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri

(2014) Jee-Hwan Oh et al.   NUCLEIC ACIDS RESEARCH

sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites

(2014) Shengsong Xie et al.   PLoS One

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

(2014) P. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

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

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

Phosphotransferase System-Mediated Glucose Uptake Is Repressed in Phosphoglucoisomerase-Deficient Corynebacterium glutamicum Strains

(2013) Steffen N. Lindner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder 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

Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2

(2013) Zihni Arslan et al.   NUCLEIC ACIDS RESEARCH

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Modular optimization of multi-gene pathways for fatty acids production in E. coli

(2013) Peng Xu et al.   Nature Communications

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

(2013) Fahim Farzadfard et al.   ACS Synthetic Biology

The natural stilbenoid pinosylvin and activated neutrophils: effects on oxidative burst, protein kinase C, apoptosis and efficiency in adjuvant arthritis

(2012) Viera Jančinová et al.   ACTA PHARMACOLOGICA SINICA

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Genome-scale genetic manipulation methods for exploring bacterial molecular biology

(2012) Alla Gagarinova et al.   Molecular BioSystems

Natural stilbenoids: distribution in the plant kingdom and chemotaxonomic interest in Vitaceae

(2012) Céline Rivière et al.   NATURAL PRODUCT REPORTS

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Optimization of butanol production from tropical maize stalk juice by fermentation with Clostridium beijerinckii NCIMB 8052

(2011) Yi Wang et al.   BIORESOURCE TECHNOLOGY

Metabolic engineering of microbial pathways for advanced biofuels production

(2011) Fuzhong Zhang et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome Engineering With Zinc-Finger Nucleases

(2011) Dana Carroll   GENETICS

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Metabolic changes in a pyruvate kinase gene deletion mutant of Corynebacterium glutamicum ATCC 13032

(2010) Kazunori Sawada et al.   METABOLIC ENGINEERING

The path to next generation biofuels: successes and challenges in the era of synthetic biology

(2010) Clementina Dellomonaco et al.   Microbial Cell Factories

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

New microbial fuels: a biotech perspective

(2009) Mathew A Rude et al.   CURRENT OPINION IN MICROBIOLOGY

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

Clinical Recognition and Diagnosis ofClostridium difficileInfection

(2008) John G. Bartlett et al.   CLINICAL INFECTIOUS DISEASES

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

(2008) Sung Kuk Lee et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli

(2008) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA