Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes

Exploiting a conjugative endogenous CRISPR-Cas3 system to tackle multidrug-resistant Klebsiella pneumoniae

(2023) Ying Zhou et al.   EBioMedicine

Regulation of CRISPR-Associated Genes by Rv1776c (CasR) in Mycobacterium tuberculosis

(2023) Wenping Wei et al.   Biomolecules

Characteristics of subtype III-A CRISPR-Cas system in Mycobacterium tuberculosis: An overview

(2023) Insaf Hamdi et al.   INFECTION GENETICS AND EVOLUTION

Sustainable manufacturing with synthetic biology

(2022) Corinne D. Scown et al.   NATURE BIOTECHNOLOGY

Alternative functions of CRISPR–Cas systems in the evolutionary arms race

(2022) Prarthana Mohanraju et al.   NATURE REVIEWS MICROBIOLOGY

Structural basis for DNA targeting by the Tn7 transposon

(2022) Yao Shen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella

(2022) Yuqiao Zhou et al.   Frontiers in Microbiology

The Bacterial Cell Wall: From Lipid II Flipping to Polymerization

(2022) Sujeet Kumar et al.   CHEMICAL REVIEWS

SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing

(2022) Pengli Cai et al.   Microbial Cell Factories

Development and application of a fast and efficient CRISPR-based genetic toolkit in Bacillus amyloliquefaciens LB1ba02

(2022) Qinglong Xin et al.   Microbial Cell Factories

A toolkit for microbial community editing

(2022) Susannah G. Tringe   NATURE REVIEWS MICROBIOLOGY

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

(2022) Grant A Rybnicky et al.   NUCLEIC ACIDS RESEARCH

Mycobacterium tuberculosis PPE51 Inhibits Autophagy by Suppressing Toll-Like Receptor 2-Dependent Signaling

(2022) Emily J. Strong et al.   mBio

Exploiting the Type I-B CRISPR Genome Editing System in Thermoanaerobacterium aotearoense SCUT27 and Engineering the Strain for Enhanced Ethanol Production

(2022) Kaiqun Dai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools

(2022) Chunyi Hu et al.   MOLECULAR CELL

Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences

(2022) Zhou-Hua Cheng et al.   NUCLEIC ACIDS RESEARCH

Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium

(2022) Meichen Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas in Acinetobacter baumannii Contributes to Antibiotic Susceptibility by Targeting Endogenous AbaI

(2022) Yuhang Wang et al.   Microbiology Spectrum

A Gene Circuit Combining the Endogenous I-E Type CRISPR-Cas System and a Light Sensor to Produce Poly-β-Hydroxybutyric Acid Efficiently

(2022) Xiaomeng Li et al.   Biosensors-Basel

RNA-activated protein cleavage with a CRISPR-associated endopeptidase

(2022) Jonathan Strecker et al.   SCIENCE

Inducible expression of large gRNA arrays for multiplexed CRISPRai applications

(2022) William M. Shaw et al.   Nature Communications

Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon

(2022) Francisco Tenjo-Castaño et al.   Nature Communications

Characterization of the self-targeting Type IV CRISPR interference system in Pseudomonas oleovorans

(2022) Xiaohan Guo et al.   Nature Microbiology

CRISPR-Cas13 technology portfolio and alliance with other genetic tools

(2022) Shimin Wu et al.   BIOTECHNOLOGY ADVANCES

Miniature CRISPR-Cas12 endonucleases – Programmed DNA targeting in a smaller package

(2022) Giang T. Nguyen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Efficiency of CRISPR-Cas9 genetic engineering in Escherichia coli BL21 is impaired by lack of Lon protease

(2022) Mira Okshevsky et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Discovery and characterization of novel type I-D CRISPR-guided transposons identified among diverse Tn7-like elements in cyanobacteria

(2022) Shan-Chi Hsieh et al.   NUCLEIC ACIDS RESEARCH

Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators

(2022) Xueyang Dong et al.   Nature Communications

Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system

(2022) Anna A. Shiriaeva et al.   Science Advances

CRISPR/Cas14 provides a promising platform in facile and versatile aptasensing with improved sensitivity

(2022) Bin Zhou et al.   TALANTA

Repurposing the Endogenous Type I-E CRISPR/Cas System for Gene Repression in Gluconobacter oxydans WSH-003

(2021) Zhijie Qin et al.   ACS Synthetic Biology

Transposon-Associated CRISPR-Cas System: A Powerful DNA Insertion Tool

(2021) Wang Ma et al.   TRENDS IN MICROBIOLOGY

Exploiting heterologous and endogenous CRISPR‐Cas systems for genome editing in the probiotic Clostridium butyricum

(2021) Xiuqing Zhou et al.   BIOTECHNOLOGY AND BIOENGINEERING

Dual modes of CRISPR-associated transposon homing

(2021) Makoto Saito et al.   CELL

crRNA complementarity shifts endogenous CRISPR-Cas systems between transcriptional repression and DNA defense

(2021) Hannah K. Ratner et al.   RNA Biology

Analysis of chromatid-break-repair detects a homologous recombination to non-homologous end-joining switch with increasing load of DNA double-strand breaks

(2021) Tamara Murmann-Konda et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Orthogonal CRISPR-associated transposases for parallel and multiplexed chromosomal integration

(2021) Siqi Yang et al.   NUCLEIC ACIDS RESEARCH

The PshX subunit of the photochemical reaction center from Heliobacterium modesticaldum acts as a low-energy antenna

(2021) Gregory S. Orf et al.   PHOTOSYNTHESIS RESEARCH

CASPredict: a web service for identifying Cas proteins

(2021) Shanshan Yang et al.   PeerJ

CRISPRclassify: Repeat-Based Classification of CRISPR Loci

(2021) Matthew A. Nethery et al.   CRISPR Journal

Endogenous CRISPR-assisted microhomology-mediated end joining enables rapid genome editing in Zymomonas mobilis

(2021) Xin Sui et al.   Biotechnology for Biofuels

The CRISPR-Cas toolbox and gene editing technologies

(2021) Guanwen Liu et al.   MOLECULAR CELL

Highly efficient genome editing in Xanthomonas oryzae pv.  oryzae through repurposing the endogenous type I‐C CRISPR‐Cas system

(2021) Dandan Jiang et al.   MOLECULAR PLANT PATHOLOGY

Target site selection and remodelling by type V CRISPR-transposon systems

(2021) Irma Querques et al.   NATURE

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

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

CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

(2020) Muhammad Kamruzzaman et al.   Frontiers in Microbiology

Enhancing plasmid transformation efficiency and enabling CRISPR‐Cas9/Cpf1‐based genome editing in Clostridium tyrobutyricum

(2020) Jie Zhang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Harnessing the type I CRISPR‐Cas systems for genome editing in prokaryotes

(2020) Zeling Xu et al.   ENVIRONMENTAL MICROBIOLOGY

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses

(2020) Le Huang et al.   NUCLEIC ACIDS RESEARCH

Casboundary: automated definition of integral Cas cassettes

(2020) Victor A Padilha et al.   BIOINFORMATICS

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

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

CRISPRidentify: identification of CRISPR arrays using machine learning approach

(2020) Alexander Mitrofanov et al.   NUCLEIC ACIDS RESEARCH

A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy

(2020) Jichao Wang et al.   NUCLEIC ACIDS RESEARCH

CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci

(2020) Jakob Russel et al.   CRISPR Journal

Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation

(2019) Adrien LS Jacquin et al.   BIOINFORMATICS

CRISPR-Cas, a highly effective tool for genome editing in Clostridium saccharoperbutylacetonicum N1-4(HMT)

(2019) Aretha N Atmadjaja et al.   FEMS MICROBIOLOGY LETTERS

CRISPRi as an efficient tool for gene repression in archaea

(2019) Aris-Edda Stachler et al.   METHODS

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

Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus

(2019) Claudio Hidalgo-Cantabrana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Generation of a fully erythromycin-sensitive strain of Clostridioides difficile using a novel CRISPR-Cas9 genome editing system

(2019) Patrick Ingle et al.   Scientific Reports

Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis

(2019) Dingyu Liu et al.   Biotechnology for Biofuels

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

CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing

(2019) Samuele Cancellieri et al.   BIOINFORMATICS

Fidelity of prespacer capture and processing is governed by the PAM mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system

(2019) Kakimani Nagarajan Yoganand et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering

(2019) Yanli Zheng et al.   NUCLEIC ACIDS RESEARCH

Endogenous CRISPR-Cas System-Based Genome Editing and Antimicrobials: Review and Prospects

(2019) Yingjun Li et al.   Frontiers in Microbiology

Structural basis of DNA targeting by a transposon-encoded CRISPR–Cas system

(2019) Tyler S. Halpin-Healy et al.   NATURE

Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

(2018) Jie Zhang et al.   METABOLIC ENGINEERING

Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays

(2018) Hayun Lee et al.   MOLECULAR CELL

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Advances in Industrial Biotechnology Using CRISPR-Cas Systems

(2018) Paul D. Donohoue et al.   TRENDS IN BIOTECHNOLOGY

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

In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences

(2018) Brian J. Mendoza et al.   Biotechnology Journal

PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures

(2018) Daniel Gleditzsch et al.   RNA Biology

CRISPR RNA-guided DNA cleavage by reconstituted Type I-A immune effector complexes

(2018) Sonali Majumdar et al.   EXTREMOPHILES

Genome editing in Streptococcus mutans through self-targeting CRISPR arrays

(2018) Tao Gong et al.   Molecular Oral Microbiology

Deciphering, Communicating, and Engineering the CRISPR PAM

(2017) Ryan T. Leenay et al.   JOURNAL OF MOLECULAR BIOLOGY

Recruitment of CRISPR-Cas systems by Tn7-like transposons

(2017) Joseph E. Peters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type III CRISPR-Cas Immunity: Major Differences Brushed Aside

(2017) Gintautas Tamulaitis et al.   TRENDS IN MICROBIOLOGY

Characterizing leader sequences of CRISPR loci

(2016) Omer S. Alkhnbashi et al.   BIOINFORMATICS

CRISPR technologies for bacterial systems: Current achievements and future directions

(2016) Kyeong Rok Choi et al.   BIOTECHNOLOGY ADVANCES

Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex

(2016) Sonali Majumdar et al.   EXTREMOPHILES

Gene Repression in Haloarchaea Using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas I-B System

(2016) Aris-Edda Stachler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

(2016) Ryan T. Leenay et al.   MOLECULAR CELL

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system

(2016) Daniel Gleditzsch et al.   NUCLEIC ACIDS RESEARCH

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Bacteria vs. Bacteriophages: Parallel Evolution of Immune Arsenals

(2016) Muhammad A. B. Shabbir et al.   Frontiers in Microbiology

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

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

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

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

Whole-genome analysis of an oxacillin-susceptible CC80mecA-positiveStaphylococcus aureusclinical isolate: insights into the mechanisms of cryptic methicillin resistance

(2015) Artur J. Sabat et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

(2015) Raj Chari et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

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

Harnessing Type I and Type III CRISPR-Cas systems for genome editing

(2015) Yingjun Li et al.   NUCLEIC ACIDS RESEARCH

Three CRISPR-Cas immune effector complexes coexist inPyrococcus furiosus

(2015) Sonali Majumdar et al.   RNA

The subtype I-F CRISPR–Cas system influences pathogenicity island retention inPectobacterium atrosepticumvia crRNA generation and Csy complex formation

(2015) Corinna Richter et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

(2015) Sergey V. Prykhozhij et al.   PLoS One

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

CasOT: a genome-wide Cas9/gRNA off-target searching tool

(2014) A. Xiao et al.   BIOINFORMATICS

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Efficient programmable gene silencing by Cascade

(2014) Devashish Rath et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages

(2014) Bruno Martel et al.   NUCLEIC ACIDS RESEARCH

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

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

CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri

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

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

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

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

A CRISPR/Cas system mediates bacterial innate immune evasion and virulence

(2013) Timothy R. Sampson et al.   NATURE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing inSulfolobus islandicus

(2013) Wenfang Peng et al.   RNA Biology

Programmable plasmid interference by the CRISPR-Cas system inThermococcus kodakarensis

(2013) Joshua R. Elmore et al.   RNA Biology

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome Analyses of Icelandic Strains of Sulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies

(2011) L. Guo et al.   JOURNAL OF BACTERIOLOGY

Identification and characterization ofE. coliCRISPR-caspromoters and their silencing by H-NS

(2010) Ümit Pul et al.   MOLECULAR MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS