IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-30685-x.html
   My bibliography  Save this article

A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors

Author

Listed:
  • Dorothy Koveal

    (Harvard Medical School)

  • Paul C. Rosen

    (Harvard Medical School
    Massachusetts Institute of Technology)

  • Dylan J. Meyer

    (Harvard Medical School)

  • Carlos Manlio Díaz-García

    (Harvard Medical School
    University of Oklahoma Health Sciences Center)

  • Yongcheng Wang

    (Harvard University
    Zhejiang University Medical Center)

  • Li-Heng Cai

    (Harvard University
    University of Virginia)

  • Peter J. Chou

    (Harvard Medical School
    Stanford University School of Medicine)

  • David A. Weitz

    (Harvard University)

  • Gary Yellen

    (Harvard Medical School)

Abstract

Genetically encoded fluorescent biosensors are powerful tools used to track chemical processes in intact biological systems. However, the development and optimization of biosensors remains a challenging and labor-intensive process, primarily due to technical limitations of methods for screening candidate biosensors. Here we describe a screening modality that combines droplet microfluidics and automated fluorescence imaging to provide an order of magnitude increase in screening throughput. Moreover, unlike current techniques that are limited to screening for a single biosensor feature at a time (e.g. brightness), our method enables evaluation of multiple features (e.g. contrast, affinity, specificity) in parallel. Because biosensor features can covary, this capability is essential for rapid optimization. We use this system to generate a high-performance biosensor for lactate that can be used to quantify intracellular lactate concentrations. This biosensor, named LiLac, constitutes a significant advance in metabolite sensing and demonstrates the power of our screening approach.

Suggested Citation

  • Dorothy Koveal & Paul C. Rosen & Dylan J. Meyer & Carlos Manlio Díaz-García & Yongcheng Wang & Li-Heng Cai & Peter J. Chou & David A. Weitz & Gary Yellen, 2022. "A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30685-x
    DOI: 10.1038/s41467-022-30685-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-30685-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-30685-x?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. Mark A. Lobas & Rongkun Tao & Jun Nagai & Mira T. Kronschläger & Philip M. Borden & Jonathan S. Marvin & Loren L. Looger & Baljit S. Khakh, 2019. "A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    2. Joachim Goedhart & David von Stetten & Marjolaine Noirclerc-Savoye & Mickaël Lelimousin & Linda Joosen & Mark A. Hink & Laura van Weeren & Theodorus W.J. Gadella & Antoine Royant, 2012. "Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
    3. Sheng Hui & Jonathan M. Ghergurovich & Raphael J. Morscher & Cholsoon Jang & Xin Teng & Wenyun Lu & Lourdes A. Esparza & Tannishtha Reya & Le Zhan & Jessie Yanxiang Guo & Eileen White & Joshua D. Rabi, 2017. "Glucose feeds the TCA cycle via circulating lactate," Nature, Nature, vol. 551(7678), pages 115-118, November.
    4. Franka H. Linden & Eike K. Mahlandt & Janine J. G. Arts & Joep Beumer & Jens Puschhof & Saskia M. A. Man & Anna O. Chertkova & Bas Ponsioen & Hans Clevers & Jaap D. Buul & Marten Postma & Theodorus W., 2021. "A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. Dana C. Nadler & Stacy-Anne Morgan & Avi Flamholz & Kaitlyn E. Kortright & David F. Savage, 2016. "Rapid construction of metabolite biosensors using domain-insertion profiling," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    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. Zhong Guo & Oleh Smutok & Wayne A. Johnston & Patricia Walden & Jacobus P. J. Ungerer & Thomas S. Peat & Janet Newman & Jake Parker & Tom Nebl & Caryn Hepburn & Artem Melman & Richard J. Suderman & Ev, 2021. "Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Thanh-an Pham & Aleix Boquet-Pujadas & Sandip Mondal & Michael Unser & George Barbastathis, 2024. "Deep-prior ODEs augment fluorescence imaging with chemical sensors," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Jin Wang & Ning Xue & Wenjia Pan & Ran Tu & Shixin Li & Yue Zhang & Yufeng Mao & Ye Liu & Haijiao Cheng & Yanmei Guo & Wei Yuan & Xiaomeng Ni & Meng Wang, 2023. "Repurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    4. 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.
    5. Danielle L. Schmitt & Stephanie D. Curtis & Anne C. Lyons & Jin-fan Zhang & Mingyuan Chen & Catherine Y. He & Sohum Mehta & Reuben J. Shaw & Jin Zhang, 2022. "Spatial regulation of AMPK signaling revealed by a sensitive kinase activity reporter," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    6. Charlotte M. François & Thomas Pihl & Marion Dunoyer de Segonzac & Chloé Hérault & Bruno Hudry, 2023. "Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Liyuan Zhu & Harold M. McNamara & Jared E. Toettcher, 2023. "Light-switchable transcription factors obtained by direct screening in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    8. Ali Vaziri-Gohar & Jonathan J. Hue & Ata Abbas & Hallie J. Graor & Omid Hajihassani & Mehrdad Zarei & George Titomihelakis & John Feczko & Moeez Rathore & Sylwia Chelstowska & Alexander W. Loftus & Ru, 2023. "Increased glucose availability sensitizes pancreatic cancer to chemotherapy," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    9. Shannon Trombley & Jackson Powell & Pavithran Guttipatti & Andrew Matamoros & Xiaohui Lin & Tristan O’Harrow & Tobias Steinschaden & Leann Miles & Qin Wang & Shuchao Wang & Jingyun Qiu & Qingyang Li &, 2023. "Glia instruct axon regeneration via a ternary modulation of neuronal calcium channels in Drosophila," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    10. Xinyue Mu & Trent D. Evans & Fuzhong Zhang, 2024. "ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    11. Taijin Lan & Sara Arastu & Jarrick Lam & Hyungsin Kim & Wenping Wang & Samuel Wang & Vrushank Bhatt & Eduardo Cararo Lopes & Zhixian Hu & Michael Sun & Xuefei Luo & Jonathan M. Ghergurovich & Xiaoyang, 2024. "Glucose-6-phosphate dehydrogenase maintains redox homeostasis and biosynthesis in LKB1-deficient KRAS-driven lung cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    12. Kirsty J Martin & Ewan J McGhee & Juliana P Schwarz & Martin Drysdale & Saskia M Brachmann & Volker Stucke & Owen J Sansom & Kurt I Anderson, 2018. "Accepting from the best donor; analysis of long-lifetime donor fluorescent protein pairings to optimise dynamic FLIM-based FRET experiments," PLOS ONE, Public Library of Science, vol. 13(1), pages 1-25, January.
    13. Sina Rhein & Riccardo Costalunga & Julica Inderhees & Tammo Gürtzgen & Teresa Christina Faupel & Zaib Shaheryar & Adriana Arrulo Pereira & Alaa Othman & Kimberly Begemann & Sonja Binder & Ines Stöltin, 2024. "The reactive pyruvate metabolite dimethylglyoxal mediates neurological consequences of diabetes," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    14. Willow Coyote-Maestas & David Nedrud & Antonio Suma & Yungui He & Kenneth A. Matreyek & Douglas M. Fowler & Vincenzo Carnevale & Chad L. Myers & Daniel Schmidt, 2021. "Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    15. Anna Rubinski & Noam E Ziv, 2015. "Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses," PLOS Computational Biology, Public Library of Science, vol. 11(11), pages 1-29, November.
    16. Xueman Chen & Rong Luo & Yunmei Zhang & Shuying Ye & Xin Zeng & Jiang Liu & Di Huang & Yujie Liu & Qiang Liu & Man-Li Luo & Erwei Song, 2022. "Long noncoding RNA DIO3OS induces glycolytic-dominant metabolic reprogramming to promote aromatase inhibitor resistance in breast cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    17. Juewon Kim & Yunju Jo & Gyumin Lim & Yosep Ji & Jong-Hwa Roh & Wan-Gi Kim & Hyon-Seung Yi & Dong Wook Choi & Donghyun Cho & Dongryeol Ryu, 2024. "A microbiota-derived metabolite, 3-phenyllactic acid, prolongs healthspan by enhancing mitochondrial function and stress resilience via SKN-1/ATFS-1 in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    18. Noran Abdel Wadood & Monika I. Hollenhorst & Mohamed Ibrahem Elhawy & Na Zhao & Clara Englisch & Saskia B. Evers & Mahana Sabachvili & Stephan Maxeiner & Amanda Wyatt & Christian Herr & Ann-Kathrin Bu, 2025. "Tracheal tuft cells release ATP and link innate to adaptive immunity in pneumonia," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    19. Takayuki Miki & Masahiro Hashimoto & Hiroki Takahashi & Masatoshi Shimizu & Sae Nakayama & Tadaomi Furuta & Hisakazu Mihara, 2024. "De novo designed YK peptides forming reversible amyloid for synthetic protein condensates in mammalian cells," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    20. Pierre Millard & Uwe Schmitt & Patrick Kiefer & Julia A Vorholt & Stéphanie Heux & Jean-Charles Portais, 2020. "ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks," PLOS Computational Biology, Public Library of Science, vol. 16(4), pages 1-18, April.

    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_s41467-022-30685-x. 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.