A Novel and Efficient Method for Bacteria Genome Editing Employing both CRISPR/Cas9 and an Antibiotic Resistance Cassette

Zhang, Hong; Cheng, Qiu Xiang; Liu, Ai Min; Zhao, Guo Ping; Wang, Jing‐Zhi

doi:10.3389/fmicb.2017.00812

Cited by 42 publications

(23 citation statements)

References 24 publications

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“…Nevertheless, the CRISPR/Cas9 technology has been exploited for a broad range of bacteria and algae. Examples include Escherichia coli , Streptococcus pneumoniae , Bacillus subtilis , B. smithii , Streptomyces spp., Lactobacillus reuteri , L. casei , Clostridium beijerinckii , C. ljungdahlii , C. acetobutylicum , C. cellulolyticum , Pseudomonas putida , Synechococcus elongatus , Actinoplanes sp., Corynebacterium glutamicum , Staphylococcus aureus , and Myxococcus xanthus . These reports have demonstrated that the CRISPR/Cas9 system enables the easy and efficient establishment of point mutations, indels, gene replacements, large gene integrations, and large chromosomal deletions at target genomic loci.…”

Section: Application Of the Crispr/cas System For Microbial Metabolicmentioning

confidence: 99%

Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering

Arazoe

Kondo

Nishida

2018

Biotechnology Journal

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Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for genome editing in various organisms and cell types. Although genome editing enables efficient genome manipulations, such as gene disruptions, gene knockins, and chromosomal translocations via DNA double-strand break (DSB) repair in eukaryotes, DSBs induced by the CRISPR/Cas system are lethal or severely toxic to many microorganisms. Therefore, in many prokaryotes, including industrially useful microbes, the CRISPR/Cas system is often used as a negative selection component in combination with recombineering or other related strategies. Novel and revolutionary technologies have been recently developed to re-write targeted nucleotides (C:G to T:A and A:T to G:C) without DSBs and donor DNA templates. These technologies rely on the recruitment of deaminases at specific target loci using the nuclease-deficient CRISPR/Cas system. Here, the authors review and compare CRISPR-based genome editing, current base editing platforms and their spectra. The authors discuss how these technologies can be applied in various aspects of microbial metabolic engineering to overcome barriers to cellular regulation in prokaryotes.

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Section: Application Of the Crispr/cas System For Microbial Metabolicmentioning

confidence: 99%

Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering

Arazoe

Kondo

Nishida

2018

Biotechnology Journal

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“…Several recent studies proposed CRISPR-Cas systems for controlling antibiotic-resistant strains. 5,17,36,40 Therefore, in this review article, we aimed to review the role of the CRISPR-Cas system to promote sensitization of bacteria against antibiotics.…”

Section: Introductionmentioning

confidence: 99%

“…CRISPR-Cas systems have been identified as a bacterial adaptive immune system 41 and as analogs of the mammalian immune system. 42 In the recent studies, the CRISPR-Cas system has been used for specific genome editing and different applications including treating genetic diseases, 43 genome engineering of various bacteria, 44 plants, 45 mice, 46 flies, 47 worms, 48 and more, and reversal of antibiotic resistance by targeting resistance genes, 5,17,40 as well as integration machinery of the systems, has been used to function as a molecular recording device. 49 This interesting system is found in approximately 50% of bacterial genomes and 87% of archaeal genomes.…”

Section: Introducing Crispr-casmentioning

confidence: 99%

<p>How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance</p>

Gholizadeh¹,

Köse²,

Dao³

et al. 2020

IDR

101

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Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibioticresistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.

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“…Among all CRISPR/Cas9-based genome editing methods, CRISPR/Cas9-assisted recombineering methods perform very well. Existing CRISPR/Cas9-assisted recombineering methods use cycle DNA (plasmid-borne dsDNA) [24][25][26] or linear DNA (PCR-amplified dsDNA or synthesized ssDNA) [23,24,[27][28][29] as the editing template, and both kinds of templates have advantages and disadvantages. The cycle editing template can avoid the attack by DNA exonucleases and copy itself along with the plasmid replication, thus resulting in much higher homologous recombination efficiency and editing efficiency.…”

Section: Introductionmentioning

confidence: 99%

Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering

Huang

Guo

Wang

et al. 2020

Preprint

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Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering.

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A Novel and Efficient Method for Bacteria Genome Editing Employing both CRISPR/Cas9 and an Antibiotic Resistance Cassette

Cited by 42 publications

References 24 publications

Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering

Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering

<p>How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance</p>

Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering

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