IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31422-0.html
   My bibliography  Save this article

A plasmid system with tunable copy number

Author

Listed:
  • Miles V. Rouches

    (Cornell University)

  • Yasu Xu

    (Cornell University)

  • Louis Brian Georges Cortes

    (Cornell University)

  • Guillaume Lambert

    (Cornell University)

Abstract

Plasmids are one of the most commonly used platforms for genetic engineering and recombinant gene expression in bacteria. The range of available copy numbers for cloning vectors is largely restricted to the handful of Origins of Replication (ORIs) that have been isolated from plasmids found in nature. Here, we introduce two systems that allow for the continuous, finely-tuned control of plasmid copy number between 1 and 800 copies per cell: a plasmid with an anhydrotetracycline-controlled copy number, and a parallelized assay that is used to generate a continuous spectrum of 1194 ColE1-based copy number variants. Using these systems, we investigate the effects of plasmid copy number on cellular growth rates, gene expression, biosynthesis, and genetic circuit performance. We perform single-cell timelapse measurements to characterize plasmid loss, runaway plasmid replication, and quantify the impact of plasmid copy number on the variability of gene expression. Using our assay, we find that each plasmid imposes a 0.063% linear metabolic burden on their hosts, hinting at a simple relationship between metabolic burdens and plasmid DNA synthesis. Our systems enable the precise control of gene expression, and our results highlight the importance of tuning plasmid copy number as a powerful tool for the optimization of synthetic biological systems.

Suggested Citation

  • Miles V. Rouches & Yasu Xu & Louis Brian Georges Cortes & Guillaume Lambert, 2022. "A plasmid system with tunable copy number," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31422-0
    DOI: 10.1038/s41467-022-31422-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31422-0
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-31422-0?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. Xinyi Wan & Filipe Pinto & Luyang Yu & Baojun Wang, 2020. "Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    2. Laurent Potvin-Trottier & Nathan D. Lord & Glenn Vinnicombe & Johan Paulsson, 2016. "Synchronous long-term oscillations in a synthetic gene circuit," Nature, Nature, vol. 538(7626), pages 514-517, October.
    3. Bin Shao & Jayan Rammohan & Daniel A. Anderson & Nina Alperovich & David Ross & Christopher A. Voigt, 2021. "Single-cell measurement of plasmid copy number and promoter activity," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    4. Tanita Wein & Nils F. Hülter & Itzhak Mizrahi & Tal Dagan, 2019. "Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Shivang Hina-Nilesh Joshi & Chentao Yong & Andras Gyorgy, 2022. "Inducible plasmid copy number control for synthetic biology in commonly used E. coli strains," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Kanakov, Oleg & Chen, Shangbin & Zaikin, Alexey, 2024. "Learning by selective plasmid loss for intracellular synthetic classifiers," Chaos, Solitons & Fractals, Elsevier, vol. 179(C).
    3. Noor Radde & Genevieve A. Mortensen & Diya Bhat & Shireen Shah & Joseph J. Clements & Sean P. Leonard & Matthew J. McGuffie & Dennis M. Mishler & Jeffrey E. Barrick, 2024. "Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. 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.

    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. Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Michael B. Sheets & Nathan Tague & Mary J. Dunlop, 2023. "An optogenetic toolkit for light-inducible antibiotic resistance," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Lukas Aufinger & Johann Brenner & Friedrich C. Simmel, 2022. "Complex dynamics in a synchronized cell-free genetic clock," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    4. Lucas Henrion & Juan Andres Martinez & Vincent Vandenbroucke & Mathéo Delvenne & Samuel Telek & Andrew Zicler & Alexander Grünberger & Frank Delvigne, 2023. "Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Se Ho Park & Seokmin Ha & Jae Kyoung Kim, 2023. "A general model-based causal inference method overcomes the curse of synchrony and indirect effect," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    6. Duncan Ingram & Guy-Bart Stan, 2023. "Modelling genetic stability in engineered cell populations," Nature Communications, Nature, vol. 14(1), pages 1-12, 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. Jung Hun Park & Gábor Holló & Yolanda Schaerli, 2024. "From resonance to chaos by modulating spatiotemporal patterns through a synthetic optogenetic oscillator," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    9. Alvah Zorea & David Pellow & Liron Levin & Shai Pilosof & Jonathan Friedman & Ron Shamir & Itzhak Mizrahi, 2024. "Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Qiu E. Yang & Xiaodan Ma & Minchun Li & Mengshi Zhao & Lingshuang Zeng & Minzhen He & Hui Deng & Hanpeng Liao & Christopher Rensing & Ville-Petri Friman & Shungui Zhou & Timothy R. Walsh, 2024. "Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    11. Shivang Hina-Nilesh Joshi & Chentao Yong & Andras Gyorgy, 2022. "Inducible plasmid copy number control for synthetic biology in commonly used E. coli strains," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    12. Carolyn N. Bayer & Maja Rennig & Anja K. Ehrmann & Morten H. H. Nørholm, 2021. "A standardized genome architecture for bacterial synthetic biology (SEGA)," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    13. Yinyin Ma & Josep Ramoneda & David R. Johnson, 2023. "Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    14. J. Carlos R. Hernandez-Beltran & Jerónimo Rodríguez-Beltrán & Oscar Bruno Aguilar-Luviano & Jesús Velez-Santiago & Octavio Mondragón-Palomino & R. Craig MacLean & Ayari Fuentes-Hernández & Alvaro San , 2024. "Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    15. Jia, Jing & Zhao, Zhong & Yang, Jingen & Zeb, Anwar, 2024. "Parameter estimation and global sensitivity analysis of a bacterial-plasmid model with impulsive drug treatment," Chaos, Solitons & Fractals, Elsevier, vol. 183(C).
    16. Das, Saureesh, 2022. "Recurrence quantification and bifurcation analysis of electrical activity in resistive/memristive synapse coupled Fitzhugh–Nagumo type neurons," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).
    17. 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.
    18. Xuan Zou & Xiaohong Xiao & Ziran Mo & Yashi Ge & Xing Jiang & Ruolin Huang & Mengxue Li & Zixin Deng & Shi Chen & Lianrong Wang & Sang Yup Lee, 2022. "Systematic strategies for developing phage resistant Escherichia coli strains," Nature Communications, Nature, vol. 13(1), pages 1-12, 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:13:y:2022:i:1:d:10.1038_s41467-022-31422-0. 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.