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Engineered cytosine base editor enabling broad-scope and high-fidelity gene editing in Streptomyces

Author

Listed:
  • Jian Wang

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Ke Wang

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Zhe Deng

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Zhiyu Zhong

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Guo Sun

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Qing Mei

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Fuling Zhou

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Zixin Deng

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University)

  • Yuhui Sun

    (Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University
    Huazhong University of Science and Technology)

Abstract

Base editing (BE) faces protospacer adjacent motif (PAM) constraints and off-target effects in both eukaryotes and prokaryotes. For Streptomyces, renowned as one of the most prolific bacterial producers of antibiotics, the challenges are more pronounced due to its diverse genomic content and high GC content. Here, we develop a base editor named eSCBE3-NG-Hypa, tailored with both high efficiency and -fidelity for Streptomyces. Of note, eSCBE3-NG-Hypa recognizes NG PAM and exhibits high activity at challenging sites with high GC content or GC motifs, while displaying minimal off-target effects. To illustrate its practicability, we employ eSCBE3-NG-Hypa to achieve precise key amino acid conversion of the dehydratase (DH) domains within the modular polyketide synthase (PKS) responsible for the insecticide avermectins biosynthesis, achieving domains inactivation. The resulting DH-inactivated mutants, while ceasing avermectins production, produce a high yield of oligomycin, indicating competitive relationships among multiple biosynthetic gene clusters (BGCs) in Streptomyces avermitilis. Leveraging this insight, we use eSCBE3-NG-Hypa to introduce premature stop codons into competitor gene cluster of ave in an industrial S. avermitilis, with the mutant Δolm exhibiting the highest 4.45-fold increase in avermectin B1a compared to the control. This work provides a potent tool for modifying biosynthetic pathways and advancing metabolic engineering in Streptomyces.

Suggested Citation

  • Jian Wang & Ke Wang & Zhe Deng & Zhiyu Zhong & Guo Sun & Qing Mei & Fuling Zhou & Zixin Deng & Yuhui Sun, 2024. "Engineered cytosine base editor enabling broad-scope and high-fidelity gene editing in Streptomyces," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49987-3
    DOI: 10.1038/s41467-024-49987-3
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    1. Johnny H. Hu & Shannon M. Miller & Maarten H. Geurts & Weixin Tang & Liwei Chen & Ning Sun & Christina M. Zeina & Xue Gao & Holly A. Rees & Zhi Lin & David R. Liu, 2018. "Evolved Cas9 variants with broad PAM compatibility and high DNA specificity," Nature, Nature, vol. 556(7699), pages 57-63, April.
    2. Jungjoon K. Lee & Euihwan Jeong & Joonsun Lee & Minhee Jung & Eunji Shin & Young-hoon Kim & Kangin Lee & Inyoung Jung & Daesik Kim & Seokjoong Kim & Jin-Soo Kim, 2018. "Directed evolution of CRISPR-Cas9 to increase its specificity," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    3. Ang Li & Hitoshi Mitsunobu & Shin Yoshioka & Takahisa Suzuki & Akihiko Kondo & Keiji Nishida, 2022. "Cytosine base editing systems with minimized off-target effect and molecular size," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    4. Samuel H. Sternberg & Benjamin LaFrance & Matias Kaplan & Jennifer A. Doudna, 2015. "Conformational control of DNA target cleavage by CRISPR–Cas9," Nature, Nature, vol. 527(7576), pages 110-113, November.
    5. Samuel H. Sternberg & Sy Redding & Martin Jinek & Eric C. Greene & Jennifer A. Doudna, 2014. "DNA interrogation by the CRISPR RNA-guided endonuclease Cas9," Nature, Nature, vol. 507(7490), pages 62-67, March.
    6. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
    7. Janice S. Chen & Yavuz S. Dagdas & Benjamin P. Kleinstiver & Moira M. Welch & Alexander A. Sousa & Lucas B. Harrington & Samuel H. Sternberg & J. Keith Joung & Ahmet Yildiz & Jennifer A. Doudna, 2017. "Enhanced proofreading governs CRISPR–Cas9 targeting accuracy," Nature, Nature, vol. 550(7676), pages 407-410, October.
    8. Changyang Zhou & Yidi Sun & Rui Yan & Yajing Liu & Erwei Zuo & Chan Gu & Linxiao Han & Yu Wei & Xinde Hu & Rong Zeng & Yixue Li & Haibo Zhou & Fan Guo & Hui Yang, 2019. "Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis," Nature, Nature, vol. 571(7764), pages 275-278, July.
    9. Zhiquan Liu & Mao Chen & Siyu Chen & Jichao Deng & Yuning Song & Liangxue Lai & Zhanjun Li, 2018. "Highly efficient RNA-guided base editing in rabbit," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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