Genome Editing in Bacteria: CRISPR-Cas and Beyond

Microbial Chassis Development for Natural Product Biosynthesis

(2020) Xianhao Xu et al.   TRENDS IN BIOTECHNOLOGY

CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1

(2020) Yufeng Luo et al.   Microbial Cell Factories

Prime genome editing in rice and wheat

(2020) Qiupeng Lin et al.   NATURE BIOTECHNOLOGY

CRISPR–Cas12-based detection of SARS-CoV-2

(2020) James P. Broughton et al.   NATURE BIOTECHNOLOGY

Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing

(2020) Qiang Cheng et al.   Nature Nanotechnology

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Efficient generation of mouse models with the prime editing system

(2020) Yao Liu et al.   Cell Discovery

CRISPR with a Happy Ending: Non‐Templated DNA Repair for Prokaryotic Genome Engineering

(2020) Max Finger‐Bou et al.   Biotechnology Journal

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

An undergraduate laboratory experience using CRISPR-Cas9 technology to deactivate green fluorescent protein expression in Escherichia coli

(2019) Jay N. Pieczynski et al.   BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Accelerated genome engineering of Pseudomonas putida by I-Sce I―mediated recombination and CRISPR-Cas9 counterselection

(2019) Nicolas T. Wirth et al.   Microbial Biotechnology

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

(2019) Erwei Zuo et al.   SCIENCE

A rapid and versatile tool for genomic engineering in Lactococcus lactis

(2019) Tingting Guo et al.   Microbial Cell Factories

Development of drug-inducible CRISPR-Cas9 systems for large-scale functional screening

(2019) Ning Sun et al.   BMC GENOMICS

Development of a CRISPR/Cas9 system for Methylococcus capsulatus in vivo gene editing

(2019) Timothy Tapscott et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a RecE/T‐Assisted CRISPR–Cas9 Toolbox for Lactobacillus

(2019) He Huang et al.   Biotechnology Journal

Barriers to genome editing with CRISPR in bacteria

(2019) Justin M. Vento et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

An update of the suicide plasmid‐mediated genome editing system in Corynebacterium glutamicum

(2019) Ting Wang et al.   Microbial Biotechnology

Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly

(2019) Kaihang Wang et al.   SCIENCE

Using an Endogenous CRISPR-Cas System for Genome Editing in the Human Pathogen Clostridium difficile

(2019) Anna Maikova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR/Cas9-Assisted Seamless Genome Editing in Lactobacillus plantarum and Its Application in N-Acetylglucosamine Production

(2019) Ding Zhou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene

(2019) Patricia L. Baker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR-Cas9-assisted native end-joining editing offers a simple strategy for efficient genetic engineering in Escherichia coli

(2019) Chaoyong Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

A RecET-assisted CRISPR–Cas9 genome editing in Corynebacterium glutamicum

(2018) Bo Wang et al.   Microbial Cell Factories

Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system

(2018) Jun Sun et al.   Microbial Cell Factories

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

Single plasmid systems for inducible dual protein expression and for CRISPR-Cas9/CRISPRi gene regulation in lactic acid bacterium Lactococcus lactis

(2018) Aleš Berlec et al.   Scientific Reports

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

(2018) Suhyung Cho et al.   ACS Synthetic Biology

Deaminase-mediated multiplex genome editing in Escherichia coli

(2018) Satomi Banno et al.   Nature Microbiology

Precise and efficient genome editing in Klebsiella pneumoniae using CRISPR-Cas9 and CRISPR-assisted cytidine deaminase

(2018) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods

(2018) Ryan T. Leenay et al.   Biotechnology Journal

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Systematic investigation of CRISPR–Cas9 configurations for flexible and efficient genome editing in Corynebacterium glutamicum NRRL-B11474

(2018) R. Cameron Coates 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

Genome editing via delivery of Cas9 ribonucleoprotein

(2017) Mark A. DeWitt et al.   METHODS

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems

(2017) Mari Yamada et al.   MOLECULAR CELL

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

The initiation, propagation and dynamics of CRISPR-SpyCas9 R-loop complex

(2017) Yan Zeng et al.   NUCLEIC ACIDS RESEARCH

Rapid, Selection-Free, High-Efficiency Genome Editing in Protozoan Parasites Using CRISPR-Cas9 Ribonucleoproteins

(2017) Lia Carolina Soares Medeiros et al.   mBio

In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni

(2017) Eunji Kim et al.   Nature Communications

CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum

(2017) Yu Jiang et al.   Nature Communications

Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes

(2017) Zhen Liang et al.   Nature Communications

CRISPR/Cas9-Based Counterselection Boosts Recombineering Efficiency in Pseudomonas putida

(2017) Tomás Aparicio et al.   Biotechnology Journal

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

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

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

(2016) Josef Altenbuchner   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2016) Qi Li et al.   Biotechnology Journal

The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells

(2016) Ciaran M Lee et al.   MOLECULAR THERAPY

Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome

(2016) Maximilian Müller et al.   MOLECULAR THERAPY

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

(2016) Alexis C. Komor et al.   NATURE

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9-Based Efficient Genome Editing in Clostridium ljungdahlii, an Autotrophic Gas-Fermenting Bacterium

(2016) He Huang et al.   ACS Synthetic Biology

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

(2016) Qi Li et al.   Biotechnology Journal

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

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

Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System

(2015) Yu Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

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

(2015) Yifan Li et al.   METABOLIC ENGINEERING

Photoactivatable CRISPR-Cas9 for optogenetic genome editing

(2015) Yuta Nihongaki et al.   NATURE BIOTECHNOLOGY

An updated evolutionary classification of CRISPR–Cas systems

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

An Integrated System for Precise Genome Modification in Escherichia coli

(2015) Huseyin Tas et al.   PLoS One

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

(2015) Kathrin Schumann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli

(2015) Chris R. Reisch et al.   Scientific Reports

CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

(2015) Yaojun Tong et al.   ACS Synthetic Biology

Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases

(2015) Kylie Standage-Beier et al.   ACS Synthetic Biology

Developing Universal Genetic Tools for Rapid and Efficient Deletion Mutation in Vibrio Species Based on Suicide T-Vectors Carrying a Novel Counterselectable Marker, vmi480

(2015) Peng Luo et al.   PLoS One

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

(2014) Carolin Anders et al.   NATURE

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri

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

Is homologous recombination really an error-free process?

(2014) Josée Guirouilh-Barbat et al.   Frontiers in Genetics

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

DNA polymerases are error-prone at RecA-mediated recombination intermediates

(2013) Richard T Pomerantz et al.   CELL CYCLE

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

Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands

(2013) Reuben B. Vercoe et al.   PLoS Genetics

Stress-induced mutation via DNA breaks inEscherichia coli: A molecular mechanism with implications for evolution and medicine

(2012) Susan M. Rosenberg et al.   BIOESSAYS

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. Jinek et al.   SCIENCE

APOBEC1-Mediated Editing and Attenuation of Herpes Simplex Virus 1 DNA Indicate That Neurons Have an Antiviral Role during Herpes Simplex Encephalitis

(2011) P. Gee et al.   JOURNAL OF VIROLOGY

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

An end-joining repair mechanism in Escherichia coli

(2010) R. Chayot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ClosTron: Mutagenesis in Clostridium refined and streamlined

(2009) John T. Heap et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Recombineering: a homologous recombination-based method of genetic engineering

(2009) Shyam K Sharan et al.   Nature Protocols

Engineering Variants of the I-SceI Homing Endonuclease with Strand-specific and Site-specific DNA-nicking Activity

(2008) Yan Niu et al.   JOURNAL OF MOLECULAR BIOLOGY

The antiretroviral potency of APOBEC1 deaminase from small animal species

(2008) Terumasa Ikeda et al.   NUCLEIC ACIDS RESEARCH