ArticleNature communications2023
Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 36 citations in OpenAlex.
- Enhancing the Secretion Systems: Genetic Engineering of Super Bioagents for Effective Plant Disease Control.Biotechnology and bioengineering · 2026Review
- A Lambda Red Recombinase-Assisted CRISPR/Cas9 System for Efficient and Precise Genome Editing in Agrobacterium tumefaciens.Plant biotechnology journal · 2026Article
- Technical limitations of CRISPR-Cas9 genome editing in bacteria: challenges and future directions.Archives of microbiology · 2026Review
- Advances in CRISPR-Cas for Diagnosis and Treatment ofPathogens (Basel, Switzerland) · 2026Review
- Tailoring Cas12a functionality with a user-friendly and versatile crRNA variant toolbox.Nature communications · 2025Article
- SELECT: high-precision genome editing strategy via integration of CRISPR-Cas and DNA damage response for cross-species applications.Nucleic acids research · 2025Article
- Developing a robust genome editing tool based on an endogenous type I-B CRISPR-Cas system in Saccharopolyspora spinosa.Science China. Life sciences · 2025Article
- A CRISPR Cas12a/Cpf1 strategy to facilitate robust multiplex gene editing in Aspergillus Niger.Fungal biology and biotechnology · 2025Article
- Make-or-break prime editing for genome engineering in Streptococcus pneumoniae.Nature communications · 2025Article
- Harnessing the Streptomyces-originating type I-E CRISPR/Cas system for efficient genome editing in Streptomyces.Science China. Life sciences · 2025Article
- Precision engineering of the probioticApplied and environmental microbiology · 2025Article
- Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice.Nature microbiology · 2025Article
- Tunable control of Cas12 activity promotes universal and fast one-pot nucleic acid detection.Nature communications · 2025Article
- One-for-all gene inactivation via PAM-independent base editing in bacteria.The Journal of biological chemistry · 2025Article
- Binding-driven forward tearing protospacer activated CRISPR-Cas12a system and applications for microRNA detection.Journal of nanobiotechnology · 2024Article
- A toolbox to engineer the highly productive cyanobacterium Synechococcus sp. PCC 11901.Plant physiology · 2024Article
- The rise and future of CRISPR-based approaches for high-throughput genomics.FEMS microbiology reviews · 2024Review
- An expanded genetic toolkit for inducible expression and targeted gene silencing inJournal of bacteriology · 2024Article
- Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity.Nucleic acids research · 2024Article
- Flexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope.Nature communications · 2024Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial genome editing commonly relies on chromosomal cleavage with Cas nucleases to counter-select against unedited cells. However, editing normally requires efficient recombination and high transformation efficiencies, which are unavailable in most strains. Here, we show that systematically attenuating DNA targeting activity enables RecA-mediated repair in different bacteria, allowing chromosomal cleavage to drive genome editing. Attenuation can be achieved by altering the format or expression strength of guide (g)RNAs; using nucleases with reduced cleavage activity; or engineering attenuated gRNAs (atgRNAs) with disruptive hairpins, perturbed nuclease-binding scaffolds, non-canonical PAMs, or guide mismatches. These modifications greatly increase cell counts and even improve the efficiency of different types of edits for Cas9 and Cas12a in Escherichia coli and Klebsiella oxytoca. We further apply atgRNAs to restore ampicillin sensitivity in Klebsiella pneumoniae, establishing a resistance marker for genetic studies. Attenuating DNA targeting thus offers a counterintuitive means to achieve CRISPR-driven editing across bacteria.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.