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Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria

Author

Listed:
  • Chen Dong

    (University of Washington)

  • Jason Fontana

    (University of Washington)

  • Anika Patel

    (University of Washington)

  • James M. Carothers

    (University of Washington
    University of Washington
    University of Washington)

  • Jesse G. Zalatan

    (University of Washington
    University of Washington
    University of Washington)

Abstract

Methods to regulate gene expression programs in bacterial cells are limited by the absence of effective gene activators. To address this challenge, we have developed synthetic bacterial transcriptional activators in E. coli by linking activation domains to programmable CRISPR-Cas DNA binding domains. Effective gene activation requires target sites situated in a narrow region just upstream of the transcription start site, in sharp contrast to the relatively flexible target site requirements for gene activation in eukaryotic cells. Together with existing tools for CRISPRi gene repression, these bacterial activators enable programmable control over multiple genes with simultaneous activation and repression. Further, the entire gene expression program can be switched on by inducing expression of the CRISPR-Cas system. This work will provide a foundation for engineering synthetic bacterial cellular devices with applications including diagnostics, therapeutics, and industrial biosynthesis.

Suggested Citation

  • Chen Dong & Jason Fontana & Anika Patel & James M. Carothers & Jesse G. Zalatan, 2018. "Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04901-6
    DOI: 10.1038/s41467-018-04901-6
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    Cited by:

    1. Giho Kim & Ho Joon Kim & Keonwoo Kim & Hyeon Jin Kim & Jina Yang & Sang Woo Seo, 2024. "Tunable translation-level CRISPR interference by dCas13 and engineered gRNA in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Jason Fontana & David Sparkman-Yager & Ian Faulkner & Ryan Cardiff & Cholpisit Kiattisewee & Aria Walls & Tommy G. Primo & Patrick C. Kinnunen & Hector Garcia Martin & Jesse G. Zalatan & James M. Caro, 2024. "Guide RNA structure design enables combinatorial CRISPRa programs for biosynthetic profiling," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Qun Zhou & Yatong Zhao & Changqiang Ke & Haojun Wang & Sheng Gao & Hui Li & Yan Zhang & Yang Ye & Yunzi Luo, 2024. "Repurposing endogenous type I-E CRISPR-Cas systems for natural product discovery in Streptomyces," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. William M. Shaw & Lucie Studená & Kyler Roy & Piotr Hapeta & Nicholas S. McCarty & Alicia E. Graham & Tom Ellis & Rodrigo Ledesma-Amaro, 2022. "Inducible expression of large gRNA arrays for multiplexed CRISPRai applications," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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