IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37244-y.html
   My bibliography  Save this article

Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system

Author

Listed:
  • Chenrui Qin

    (Peking University
    Peking University)

  • Yanhui Xiang

    (Chinese Academy of Sciences)

  • Jie Liu

    (Chinese Academy of Sciences)

  • Ruilin Zhang

    (Peking University)

  • Ziming Liu

    (Chinese Academy of Sciences)

  • Tingting Li

    (Chinese Academy of Sciences)

  • Zhi Sun

    (University of Chinese Academy of Science)

  • Xiaoyi Ouyang

    (Peking University)

  • Yeqing Zong

    (Bluepha Co., Ltd)

  • Haoqian M. Zhang

    (Bluepha Co., Ltd)

  • Qi Ouyang

    (Peking University)

  • Long Qian

    (Peking University)

  • Chunbo Lou

    (Chinese Academy of Sciences
    University of Chinese Academy of Science)

Abstract

Context-dependency of mammalian transcriptional elements has hindered the quantitative investigation of multigene expression stoichiometry and its biological functions. Here, we describe a host- and local DNA context-independent transcription system to gradually fine-tune single and multiple gene expression with predictable stoichiometries. The mammalian transcription system is composed of a library of modular and programmable promoters from bacteriophage and its cognate RNA polymerase (RNAP) fused to a capping enzyme. The relative expression of single genes is quantitatively determined by the relative binding affinity of the RNAP to the promoters, while multigene expression stoichiometry is predicted by a simple biochemical model with resource competition. We use these programmable and modular promoters to predictably tune the expression of three components of an influenza A virus-like particle (VLP). Optimized stoichiometry leads to a 2-fold yield of intact VLP complexes. The host-independent orthogonal transcription system provides a platform for dose-dependent control of multiple protein expression which may be applied for advanced vaccine engineering, cell-fate programming and other therapeutic applications.

Suggested Citation

  • Chenrui Qin & Yanhui Xiang & Jie Liu & Ruilin Zhang & Ziming Liu & Tingting Li & Zhi Sun & Xiaoyi Ouyang & Yeqing Zong & Haoqian M. Zhang & Qi Ouyang & Long Qian & Chunbo Lou, 2023. "Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37244-y
    DOI: 10.1038/s41467-023-37244-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37244-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-37244-y?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. Yeqing Zong & Haoqian M. Zhang & Cheng Lyu & Xiangyu Ji & Junran Hou & Xian Guo & Qi Ouyang & Chunbo Lou, 2017. "Insulated transcriptional elements enable precise design of genetic circuits," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    2. Ye Chen & Joanne M. L. Ho & David L. Shis & Chinmaya Gupta & James Long & Daniel S. Wagner & William Ott & Krešimir Josić & Matthew R. Bennett, 2018. "Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    3. Timothy Frei & Federica Cella & Fabiana Tedeschi & Joaquín Gutiérrez & Guy-Bart Stan & Mustafa Khammash & Velia Siciliano, 2020. "Characterization and mitigation of gene expression burden in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    4. Josh Tycko & Michael Wainberg & Georgi K. Marinov & Oana Ursu & Gaelen T. Hess & Braeden K. Ego & Aradhana & Amy Li & Alisa Truong & Alexandro E. Trevino & Kaitlyn Spees & David Yao & Irene M. Kaplow , 2019. "Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    5. Mark C. Leake & Jennifer H. Chandler & George H. Wadhams & Fan Bai & Richard M. Berry & Judith P. Armitage, 2006. "Stoichiometry and turnover in single, functioning membrane protein complexes," Nature, Nature, vol. 443(7109), pages 355-358, September.
    6. Roberto Di Blasi & Masue M. Marbiah & Velia Siciliano & Karen Polizzi & Francesca Ceroni, 2021. "A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    7. Ross D. Jones & Yili Qian & Velia Siciliano & Breanna DiAndreth & Jin Huh & Ron Weiss & Domitilla Del Vecchio, 2020. "An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-16, 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. Roberto Di Blasi & Mara Pisani & Fabiana Tedeschi & Masue M. Marbiah & Karen Polizzi & Simone Furini & Velia Siciliano & Francesca Ceroni, 2023. "Resource-aware construct design in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-10, 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. Roberto Di Blasi & Mara Pisani & Fabiana Tedeschi & Masue M. Marbiah & Karen Polizzi & Simone Furini & Velia Siciliano & Francesca Ceroni, 2023. "Resource-aware construct design in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Anna-Maria Makri Pistikou & Glenn A. O. Cremers & Bryan L. Nathalia & Theodorus J. Meuleman & Bas W. A. Bögels & Bruno V. Eijkens & Anne Dreu & Maarten T. H. Bezembinder & Oscar M. J. A. Stassen & Car, 2023. "Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. 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.
    4. Carlos Barajas & Hsin-Ho Huang & Jesse Gibson & Luis Sandoval & Domitilla Vecchio, 2022. "Feedforward growth rate control mitigates gene activation burden," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    5. Ross D. Jones & Yili Qian & Katherine Ilia & Benjamin Wang & Michael T. Laub & Domitilla Del Vecchio & Ron Weiss, 2022. "Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Alexendar R. Perez & Laura Sala & Richard K. Perez & Joana A. Vidigal, 2021. "CSC software corrects off-target mediated gRNA depletion in CRISPR-Cas9 essentiality screens," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    7. Jie Li & Haonan Zhang & Dongyu Li & Ya-Jun Liu & Edward A. Bayer & Qiu Cui & Yingang Feng & Ping Zhu, 2023. "Structure of the transcription open complex of distinct σI factors," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    9. Xiaolong Cheng & Zexu Li & Ruocheng Shan & Zihan Li & Shengnan Wang & Wenchang Zhao & Han Zhang & Lumen Chao & Jian Peng & Teng Fei & Wei Li, 2023. "Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    10. Annabel K. Sangree & Audrey L. Griffith & Zsofia M. Szegletes & Priyanka Roy & Peter C. DeWeirdt & Mudra Hegde & Abby V. McGee & Ruth E. Hanna & John G. Doench, 2022. "Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    11. Andras Gyorgy, 2023. "Competition and evolutionary selection among core regulatory motifs in gene expression control," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    12. Breanna DiAndreth & Noreen Wauford & Eileen Hu & Sebastian Palacios & Ron Weiss, 2022. "PERSIST platform provides programmable RNA regulation using CRISPR endoRNases," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    13. Stanislav Anastassov & Maurice Filo & Ching-Hsiang Chang & Mustafa Khammash, 2023. "A cybergenetic framework for engineering intein-mediated integral feedback control systems," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    14. Shunsuke Kawasaki & Hiroki Ono & Moe Hirosawa & Takeru Kuwabara & Shunsuke Sumi & Suji Lee & Knut Woltjen & Hirohide Saito, 2023. "Programmable mammalian translational modulators by CRISPR-associated proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    15. Cyril F Reboul & Daniel A Andrews & Musammat F Nahar & Ashley M Buckle & Anna Roujeinikova, 2011. "Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor," PLOS ONE, Public Library of Science, vol. 6(4), pages 1-7, April.
    16. 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.
    17. Navish Wadhwa & Alberto Sassi & Howard C. Berg & Yuhai Tu, 2022. "A multi-state dynamic process confers mechano-adaptation to a biological nanomachine," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    18. Bob Sluijs & Roel J. M. Maas & Ardjan J. Linden & Tom F. A. Greef & Wilhelm T. S. Huck, 2022. "A microfluidic optimal experimental design platform for forward design of cell-free genetic networks," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    19. Basila Moochickal Assainar & Kaushik Ragunathan & Ryan D. Baldridge, 2024. "Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    20. Sebastián Sosa-Carrillo & Henri Galez & Sara Napolitano & François Bertaux & Gregory Batt, 2023. "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches," Nature Communications, Nature, vol. 14(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:14:y:2023:i:1:d:10.1038_s41467-023-37244-y. 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.