Programmable adenine deamination in bacteria using a Cas9–adenine-deaminase fusion

Zhang, Ya; Zhang, Hongyuan; Wang, Zhipeng; Wu, Zhaowei; Wang, Yu; Tang, Na; Xu, Xuexia; Zhao, Suwen; Chen, Weizhong; Ji, Quanjiang

doi:10.1039/c9sc03784e

Cited by 25 publications

(28 citation statements)

References 43 publications

(57 reference statements)

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“…CBE and ABE have been applied in several bacteria such as Escherichia coli [ 21 , [47] , [48] , [49] , [50] , [51] , [52] ], Brucella melitensis [ 48 ], Clostridium beijerinckii [ 53 ], Corynebacterium glutamicum [ 54 ], Klebsiella pneumoniae [ 55 ] , Pseudomonas [ 56 ] , Staphylococcus [ 52 , 57 ] and Streptomyces [ [58] , [59] , [60] ] ( Table 1 ). However, PE has not been set up in bacteria yet.…”

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

“… Organism Editor type Base editing system a Target genes Editing efficiency Editing window (upstream of PAM) Ref. Escherichia coli E. coli BE3 pEcBE3 tetA, lacZ, rppH 100% −12 to −16 [ 48 ] E. coli Target-AID dCas9-CDA-UL galK, rpoB, xylB, manA, pta, tipaA 61–95% −16 to −20 (extended sgRNA = −18 to −24) [ 49 ] E. coli Cpf1-based BE dLB-Cpf1-BE SupF in shuttle vector 45–80% −7 to −13 (downstream of PAM) [ 47 ] E. coli ABE pABE lacZ, yagl, murR 66–100% −13 to −17 [ 52 ] E. coli ABE pnCas9-TadA lacZ, poxb 9.3–65.4% −12 to −17 [ 50 ] pdCas9-TadA 1.3–8.3% pnCas9-TadA + Cas9 12.7–99% Streptomyces S. coelicolor S. rapamycinicus Target-AID dCas9-CDA-UL str …”

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

“…Apart from CBE, ABE has also been adopted for E. coli [ 52 ]. ABE7.10 system successfully edited yagl , murR, and lacZ in MG1655 and DH5α strains, achieving high editing efficiency between 66% and 100% [ 52 ]. Additionally, Zhang and colleagues developed a double-check base editing system, which uses the DSB capability of Cas9 to eliminate unedited cells [ 50 ].…”

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

“…Ji group developed CBE [ 57 ] and ABE [ 52 ] systems for Staphylococcus . For CBE, pnCasSA-BEC was constructed by fusing nCas9(D10A) to rAPOBEC1 via XTEN linker [ 57 ].…”

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

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CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

Abdullah

Jiang

Hong

et al. 2020

Synthetic and Systems Biotechnology

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CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA double-strand break (DSB), triggering cellular repair systems mainly Non-homologous end-joining (NHEJ, imprecise repair) or Homology-directed repair (HDR, precise repair). However, DSB typically leads to unexpected DNA changes and lethality in some organisms. The establishment of bacteria and plants into major bio-production platforms require efficient and precise editing tools. Hence, in this review, we focus on the non-DSB and template-free genome editing, i.e., base editing (BE) and prime editing (PE) in bacteria and plants. We first highlight the development of base and prime editors and summarize their studies in bacteria and plants. We then discuss current and future applications of BE/PE in synthetic biology, crop improvement, evolutionary engineering, and metabolic engineering. Lastly, we critically consider the challenges and prospects of BE/PE in PAM specificity, editing efficiency, off-targeting, sequence specification, and editing window.

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Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

“…Ji group developed CBE [ 57 ] and ABE [ 52 ] systems for Staphylococcus . For CBE, pnCasSA-BEC was constructed by fusing nCas9(D10A) to rAPOBEC1 via XTEN linker [ 57 ].…”

Section: Dsb and Template-free Editing In Bacteriamentioning

confidence: 99%

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CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

Abdullah

Jiang

Hong

et al. 2020

Synthetic and Systems Biotechnology

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Dipicolylamine‐Zn Induced Targeting and Photo‐Eliminating of Pseudomonas aeruginosa and Drug‐Resistance Gram‐Positive Bacteria

Wang,

Cai,

Ning

et al. 2023

Adv Healthcare Materials

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The emergence of drug‐resistant bacteria, particularly resistant strains of Gram‐negative bacteria, such as Pseudomonas aeruginosa, poses significant threat to public health. Although antibacterial photodynamic therapy (APDT) is a promising strategy for combating drug‐resistant bacteria, actively targeted photosensitizers (PSs) remain unknown. In this study, a PS based on dipicolylamine (DPA), known as WZK‐DPA‐Zn, was designed for the selective identification of P. aeruginosa and drug‐resistant Gram‐positive bacteria. WZK‐DPA‐Zn exploited the synergistic effects of DPA‐Zn2+ coordination and cellular uptake, which could effectively anchor P. aeruginosa within a brief period (10 min) without interference from other Gram‐negative bacteria. Simultaneously, the cationic nature of WZK‐DPA‐Zn enhanced its interaction with Gram‐positive bacteria via electrostatic forces. Compared to traditional clinical antibiotics, WZK‐DPA‐Zn showed exceptional antibacterial activity without inducing drug resistance. This effectiveness was achieved using the APDT strategy when irradiated with white light or sunlight. The combination of WZK‐DPA‐Zn with Pluronic‐based thermosensitive hydrogel dressings (WZK‐DPA‐Zn@Gel) effectively eliminated mixed bacterial infections and accelerated wound healing, thereby achieving a synergistic effect where 1+1>2″. In summary, this study proposes a precise strategy employing DPA‐Zn as the targeting moiety of a PS, facilitating the rapid elimination of P. aeruginosa and drug‐resistant Gram‐positive bacteria using APDT.This article is protected by copyright. All rights reserved

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Recent Advances in CRISPR-Cas Technologies for Synthetic Biology

Jeong

Lee

2023

J Microbiol.

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With developments in synthetic biology, “engineering biology” has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.

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Programmable adenine deamination in bacteria using a Cas9–adenine-deaminase fusion

Abstract: We report a pABE system which enables highly efficient adenine to guanine conversion in bacteria. Key residues of a staphylopine/metal complex transporter cntBC were systematically screened via the pABE system.

Cited by 25 publications

References 43 publications

CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

Dipicolylamine‐Zn Induced Targeting and Photo‐Eliminating of Pseudomonas aeruginosa and Drug‐Resistance Gram‐Positive Bacteria

Recent Advances in CRISPR-Cas Technologies for Synthetic Biology

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