Highly efficient multiplex base editing: One-shot deactivation of eight genes in Shewanella oneidensis MR-1

Chen, Yaru; Cheng, Meijie; Li, Yan; Wang, Lin; Fang, Lixia; Cao, Yingxiu; Song, Hao

doi:10.1016/j.synbio.2022.09.005

Cited by 5 publications

(3 citation statements)

References 75 publications

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“…In the present study we developed and systematically investigated the performance and scalability of multiplexed base editing in Streptomyces . Multiplexed base editing has become a very popular method across various species for rapid engineering of complex phenotypes. − We performed a deep and systematic characterization of the editing outcomes to guide further improvements and developments of multiplexed base editing tools for nonmodel organisms, especially genetically recalcitrant ones. We show successful editing of up to 17 target sites and recovery of up to 15 stable edits after plasmid curing.…”

Section: Discussionmentioning

confidence: 99%

Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes

et al. 2023

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CRISPR tools, especially Cas9n-sgRNA guided cytidine deaminase base editors such as CRISPR-BEST, have dramatically simplified genetic manipulation of streptomycetes. One major advantage of CRISPR base editing technology is the possibility to multiplex experiments in genomically instable species. Here, we demonstrate scaled up Csy4 based multiplexed genome editing using CRISPR-mcBEST in Streptomyces coelicolor. We evaluated the system by simultaneously targeting 9, 18, and finally all 28 predicted specialized metabolite biosynthetic gene clusters in a single experiment. We present important insights into the performance of Csy4 based multiplexed genome editing at different scales. Using multiomics analysis, we investigated the systems wide effects of such extensive editing experiments and revealed great potentials and important bottlenecks of CRISPR-mcBEST. The presented analysis provides crucial data and insights toward the development of multiplexed base editing as a novel paradigm for high throughput engineering of Streptomyces chassis and beyond.

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Section: Discussionmentioning

confidence: 99%

Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes

et al. 2023

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“…Although the above base editing systems have been developed in EAMs, these systems are limited by their editing capacity, which mean that up to two target genes could be edited in one round of operation and could not meet the demands of editing more than two genes. Considering this limitation, a multi-target base editing system was designed by Chen et al 115 The multi-target base editing system relied on the simultaneous and stable co-expression of multiple gRNAs. 116 Therefore, they first evaluated the possibility of multiple gRNAs cassette expressed in a monocistronic or polycistronic, and the results showed that expressing multiple gRNAs in monocistronic has higher editing efficiency.…”

Section: Genetic Manipulation and Editing Tools For Engineering Eamsmentioning

confidence: 99%

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

Zhang,

Li,

Liu

et al. 2024

Chem. Soc. Rev.

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“…BEs can provide an effective and prospective genome editing approach for generating point mutations to control essential plant characteristics. With the creation of efficient multiple-base editing systems, efficient, precise, and targeted mutagenesis through genome editing sets the stage for the next generation of breeding strategies that will transform the future of agriculture [155]. In addition to the already discussed areas where base editing has been applied, base editing can also be used to edit organelle genomes [156][157][158][159][160].…”

Section: Conclusion Challenges and Prospectsmentioning

confidence: 99%

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding

Liang

Deng

et al. 2023

CIMB

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The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions–deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.

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Highly efficient multiplex base editing: One-shot deactivation of eight genes in Shewanella oneidensis MR-1

Cited by 5 publications

References 75 publications

Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes

Systems Analysis of Highly Multiplexed CRISPR-Base Editing in Streptomycetes

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding

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