IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-45893-w.html
   My bibliography  Save this article

Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements

Author

Listed:
  • Naoki Hayashi

    (Massachusetts Institute of Technology
    JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku)

  • Yong Lai

    (MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT)
    Research Laboratory of Electronics, MIT
    The Hong Kong University of Science and Technology, Clear Water Bay)

  • Jay Fuerte-Stone

    (The University of Chicago)

  • Mark Mimee

    (The University of Chicago
    The University of Chicago)

  • Timothy K. Lu

    (Massachusetts Institute of Technology
    MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT)
    Research Laboratory of Electronics, MIT
    Broad Institute)

Abstract

Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.

Suggested Citation

  • Naoki Hayashi & Yong Lai & Jay Fuerte-Stone & Mark Mimee & Timothy K. Lu, 2024. "Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45893-w
    DOI: 10.1038/s41467-024-45893-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-45893-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-45893-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Brian J. Caliando & Christopher A. Voigt, 2015. "Targeted DNA degradation using a CRISPR device stably carried in the host genome," Nature Communications, Nature, vol. 6(1), pages 1-10, November.
    2. Alexis J. Rovner & Adrian D. Haimovich & Spencer R. Katz & Zhe Li & Michael W. Grome & Brandon M. Gassaway & Miriam Amiram & Jaymin R. Patel & Ryan R. Gallagher & Jesse Rinehart & Farren J. Isaacs, 2015. "Correction: Corrigendum: Recoded organisms engineered to depend on synthetic amino acids," Nature, Nature, vol. 527(7577), pages 264-264, November.
    3. Alexander A. Green & Jongmin Kim & Duo Ma & Pamela A. Silver & James J. Collins & Peng Yin, 2017. "Complex cellular logic computation using ribocomputing devices," Nature, Nature, vol. 548(7665), pages 117-121, August.
    4. Nicolaas M. Angenent-Mari & Alexander S. Garruss & Luis R. Soenksen & George Church & James J. Collins, 2020. "A deep learning approach to programmable RNA switches," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    5. Alexis J. Rovner & Adrian D. Haimovich & Spencer R. Katz & Zhe Li & Michael W. Grome & Brandon M. Gassaway & Miriam Amiram & Jaymin R. Patel & Ryan R. Gallagher & Jesse Rinehart & Farren J. Isaacs, 2015. "Recoded organisms engineered to depend on synthetic amino acids," Nature, Nature, vol. 518(7537), pages 89-93, February.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Stefan A. Hoffmann & Yizhi Cai, 2024. "Engineering stringent genetic biocontainment of yeast with a protein stability switch," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Hongxia Zhao & Wenlong Ding & Jia Zang & Yang Yang & Chao Liu & Linzhen Hu & Yulin Chen & Guanglong Liu & Yu Fang & Ying Yuan & Shixian Lin, 2021. "Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Tiantian Chang & Weichao Ding & Shirui Yan & Yun Wang & Haoling Zhang & Yu Zhang & Zhi Ping & Huiming Zhang & Yijian Huang & Jiahui Zhang & Dan Wang & Wenwei Zhang & Xun Xu & Yue Shen & Xian Fu, 2023. "A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Yuting Chen & Eriona Hysolli & Anlu Chen & Stephen Casper & Songlei Liu & Kevin Yang & Chenli Liu & George Church, 2022. "Multiplex base editing to convert TAG into TAA codons in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Yuanli Gao & Lei Wang & Baojun Wang, 2023. "Customizing cellular signal processing by synthetic multi-level regulatory circuits," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Lei Pei & Michele Garfinkel & Markus Schmidt, 2022. "Bottlenecks and opportunities for synthetic biology biosafety standards," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    7. John P. Marken & Richard M. Murray, 2023. "Addressable and adaptable intercellular communication via DNA messaging," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Linlin Tang & Zhijin Tian & Jin Cheng & Yijing Zhang & Yongxiu Song & Yan Liu & Jinghao Wang & Pengfei Zhang & Yonggang Ke & Friedrich C. Simmel & Jie Song, 2023. "Circular single-stranded DNA as switchable vector for gene expression in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    9. Dalton R. George & Mark Danciu & Peter W. Davenport & Matthew R. Lakin & James Chappell & Emma K. Frow, 2024. "A bumpy road ahead for genetic biocontainment," Nature Communications, Nature, vol. 15(1), pages 1-5, December.
    10. Baiyang Liu & Christian Cuba Samaniego & Matthew R. Bennett & Elisa Franco & James Chappell, 2023. "A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    11. Luna Rizik & Loai Danial & Mouna Habib & Ron Weiss & Ramez Daniel, 2022. "Synthetic neuromorphic computing in living cells," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    12. SJ, Balaji & Babu, Suresh Chandra & Pal, Suresh, 2021. "Understanding Science and Policy Making in Agriculture: A Machine Learning Application for India," 2021 Conference, August 17-31, 2021, Virtual 315227, International Association of Agricultural Economists.
    13. Raphaël V. Gayet & Katherine Ilia & Shiva Razavi & Nathaniel D. Tippens & Makoto A. Lalwani & Kehan Zhang & Jack X. Chen & Jonathan C. Chen & Jose Vargas-Asencio & James J. Collins, 2023. "Autocatalytic base editing for RNA-responsive translational control," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    14. Evangelos-Marios Nikolados & Arin Wongprommoon & Oisin Mac Aodha & Guillaume Cambray & Diego A. Oyarzún, 2022. "Accuracy and data efficiency in deep learning models of protein expression," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    15. Rory L. Williams & Richard M. Murray, 2022. "Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45893-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.