Emergent CRISPR–Cas-based technologies for engineering non-model bacteria

Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum

(2023) Jongoh Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR technology: A decade of genome editing is only the beginning

(2023) Joy Y. Wang et al.   SCIENCE

Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing

(2023) Jianli Tao et al.   Nature Communications

Efficient CRISPR-Cas9 based cytosine base editors for phytopathogenic bacteria

(2023) Chenhao Li et al.   Communications Biology

CRISPR-based metabolic engineering in non-model microorganisms

(2022) Liangyu Lu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Structural biology of CRISPR–Cas immunity and genome editing enzymes

(2022) Joy Y. Wang et al.   NATURE REVIEWS MICROBIOLOGY

Merging automation and fundamental discovery into the design–build–test–learn cycle of nontraditional microbes

(2022) Nicolás Gurdo et al.   TRENDS IN BIOTECHNOLOGY

Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing

(2022) Daniel C. Volke et al.   Nature Communications

Developing a CRISPR‐assisted base‐editing system for genome engineering of Pseudomonas chlororaphis

(2022) Sheng‐Jie Yue et al.   Microbial Biotechnology

NT-CRISPR, combining natural transformation and CRISPR-Cas9 counterselection for markerless and scarless genome editing in Vibrio natriegens

(2022) Daniel Stukenberg et al.   Communications Biology

Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites

(2022) Jianli Tao et al.   Nature Communications

Synthetic Biology Toolbox, Including a Single-Plasmid CRISPR-Cas9 System to Biologically Engineer the Electrogenic, Metal-Resistant Bacterium Cupriavidus metallidurans CH34

(2022) Federico Turco et al.   ACS Synthetic Biology

Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing

(2022) Benjamin A. Adler et al.   Nature Microbiology

CRISPR-Cas13 technology portfolio and alliance with other genetic tools

(2022) Shimin Wu et al.   BIOTECHNOLOGY ADVANCES

Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases

(2022) Matthew T. N. Yarnall et al.   NATURE BIOTECHNOLOGY

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

(2022) Esteban Martínez-García et al.   NUCLEIC ACIDS RESEARCH

Synthetic biology of extremophiles: a new wave of biomanufacturing

(2022) Jian-Wen Ye et al.   TRENDS IN BIOTECHNOLOGY

Approaches to genetic tool development for rapid domestication of non-model microorganisms

(2021) Lauren A. Riley et al.   Biotechnology for Biofuels

Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant

(2021) Bjorn Thor Adalsteinsson et al.   Scientific Reports

CRISPR/Cas12a‐mediated genome engineering in the photosynthetic bacterium Rhodobacter capsulatus

(2021) Yang Zhang et al.   Microbial Biotechnology

Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis

(2021) Barbara Bosch et al.   CELL

A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing

(2021) Yaojun Tong et al.   Nature Communications

Enhanced prime editing systems by manipulating cellular determinants of editing outcomes

(2021) Peter J. Chen et al.   CELL

Development of a CRISPR interference system for selective gene knockdown in Acidithiobacillus ferrooxidans

(2021) Shohei Yamada et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing

(2021) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas

(2021) Constantinos Patinios et al.   NUCLEIC ACIDS RESEARCH

A Hyperthermoactive-Cas9 Editing Tool Reveals the Role of a Unique Arsenite Methyltransferase in the Arsenic Resistance System of Thermus thermophilus HB27

(2021) Giovanni Gallo et al.   mBio

Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos

(2021) Paige R Takasugi et al.   GENETICS

Species- and site-specific genome editing in complex bacterial communities

(2021) Benjamin E. Rubin et al.   Nature Microbiology

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

(2020) Christos Batianis et al.   Microbial Biotechnology

Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis

(2020) Xu-Hua Mo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

CRISPR interference-based gene repression in the plant growth promoter Paenibacillus sonchi genomovar Riograndensis SBR5

(2020) Luciana F. Brito et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2020) Yufeng Luo et al.   Microbial Cell Factories

Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides

(2020) Enrico Orsi et al.   Biotechnology for Biofuels

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

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

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Pseudomonas putida

(2020) Daniel C. Volke et al.   TRENDS IN MICROBIOLOGY

Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination

(2020) Peng-Fei Xia et al.   ACS Synthetic Biology

Genome editing of the anaerobic thermophile Thermoanaerobacter ethanolicus using thermostable Cas9

(2020) Yilin Le et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Engineering Native and Synthetic Pathways in Pseudomonas Putida for the Production of Tailored Polyhydroxyalkanoates ‡

(2020) Mariela P. Mezzina et al.   Biotechnology Journal

Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control

(2020) Wes Brown et al.   CHEMBIOCHEM

Targeted mutagenesis of multiple chromosomal regions in microbes

(2020) Bálint Csörgő et al.   CURRENT OPINION IN MICROBIOLOGY

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

Base editing: advances and therapeutic opportunities

(2020) Elizabeth M. Porto et al.   NATURE REVIEWS DRUG DISCOVERY

A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

(2020) Patricia Calero et al.   Nature Communications

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

(2020) Phuc Leo H. Vo et al.   NATURE BIOTECHNOLOGY

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

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

Bacterial NHEJ: a never ending story

(2019) Claire Bertrand et al.   MOLECULAR MICROBIOLOGY

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

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

Establishment and application of CRISPR interference to affect sporulation, hydrogen peroxide detoxification, and mannitol catabolism in the methylotrophic thermophile Bacillus methanolicus

(2019) Kerstin Schultenkämper et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications

(2019) Peng Cai et al.   Microbial Cell Factories

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications

(2019) Kutubuddin A. Molla et al.   TRENDS IN BIOTECHNOLOGY

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

(2019) Henry H. Lee et al.   Nature Microbiology

Chromosome engineering of the TCA cycle in Halomonas bluephagenesis for production of copolymers of 3-hydroxybutyrate and 3-hydroxyvalerate (PHBV)

(2019) Yong Chen et al.   METABOLIC ENGINEERING

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

RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium

(2019) Inés C. Cañadas et al.   ACS Synthetic Biology

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

Genome Engineering of Eubacterium limosum Using Expanded Genetic Tools and the CRISPR-Cas9 System

(2019) Jongoh Shin et al.   ACS Synthetic Biology

Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering

(2019) Ioannis Mougiakos et al.   Microbial Cell Factories

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

(2019) Andrew V. Anzalone et al.   NATURE

Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing

(2019) Thomas A. Hamilton et al.   Nature Communications

A CRISPR/Cas9-based genome editing system for Rhodococcus ruber TH

(2019) Youxiang Liang et al.   METABOLIC ENGINEERING

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313

(2019) Joyshree Ganguly et al.   Microbial Biotechnology

Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique

(2018) Bin Xiong et al.   Biotechnology for Biofuels

CRISPR/Cas9 editing genome of extremophile Halomonas spp.

(2018) Qin Qin et al.   METABOLIC ENGINEERING

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Engineering Halomonas species TD01 for enhanced polyhydroxyalkanoates synthesis via CRISPRi

(2017) Wei Tao et al.   Microbial Cell Factories

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

(2017) Nicole M. Gaudelli et al.   NATURE

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

(2017) Ioannis Mougiakos et al.   Nature Communications

A thermostable Cas9 with increased lifetime in human plasma

(2017) Lucas B. Harrington et al.   Nature Communications

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

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

(2016) Alexis C. Komor et al.   NATURE

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

(2016) Omar O. Abudayyeh et al.   SCIENCE

The Ssr protein (T1E_1405) fromPseudomonas putidaDOT-T1E enables oligonucleotide-based recombineering in platform strainP. putidaEM42

(2016) Tomás Aparicio et al.   Biotechnology Journal

Biotechnological domestication of pseudomonads using synthetic biology

(2014) Pablo I. Nikel et al.   NATURE REVIEWS MICROBIOLOGY

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

(2012) Rafael Silva-Rocha et al.   NUCLEIC ACIDS RESEARCH

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL