IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43173-7.html
   My bibliography  Save this article

High-resolution temporal profiling of E. coli transcriptional response

Author

Listed:
  • Arianna Miano

    (University of California San Diego)

  • Kevin Rychel

    (University of California San Diego)

  • Andrew Lezia

    (University of California San Diego)

  • Anand Sastry

    (University of California San Diego)

  • Bernhard Palsson

    (University of California San Diego
    Technical University of Denmark)

  • Jeff Hasty

    (University of California San Diego
    University of California San Diego
    University of California San Diego)

Abstract

Understanding how cells dynamically adapt to their environment is a primary focus of biology research. Temporal information about cellular behavior is often limited by both small numbers of data time-points and the methods used to analyze this data. Here, we apply unsupervised machine learning to a data set containing the activity of 1805 native promoters in E. coli measured every 10 minutes in a high-throughput microfluidic device via fluorescence time-lapse microscopy. Specifically, this data set reveals E. coli transcriptome dynamics when exposed to different heavy metal ions. We use a bioinformatics pipeline based on Independent Component Analysis (ICA) to generate insights and hypotheses from this data. We discovered three primary, time-dependent stages of promoter activation to heavy metal stress (fast, intermediate, and steady). Furthermore, we uncovered a global strategy E. coli uses to reallocate resources from stress-related promoters to growth-related promoters following exposure to heavy metal stress.

Suggested Citation

  • Arianna Miano & Kevin Rychel & Andrew Lezia & Anand Sastry & Bernhard Palsson & Jeff Hasty, 2023. "High-resolution temporal profiling of E. coli transcriptional response," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43173-7
    DOI: 10.1038/s41467-023-43173-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43173-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-43173-7?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. Alexandra Gennaris & Benjamin Ezraty & Camille Henry & Rym Agrebi & Alexandra Vergnes & Emmanuel Oheix & Julia Bos & Pauline Leverrier & Leon Espinosa & Joanna Szewczyk & Didier Vertommen & Olga Iranz, 2015. "Repairing oxidized proteins in the bacterial envelope using respiratory chain electrons," Nature, Nature, vol. 528(7582), pages 409-412, December.
    2. Kevin Rychel & Anand V. Sastry & Bernhard O. Palsson, 2020. "Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    3. Anand V. Sastry & Ye Gao & Richard Szubin & Ying Hefner & Sibei Xu & Donghyuk Kim & Kumari Sonal Choudhary & Laurence Yang & Zachary A. King & Bernhard O. Palsson, 2019. "The Escherichia coli transcriptome mostly consists of independently regulated modules," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    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. Arjun Patel & Dominic McGrosso & Ying Hefner & Anaamika Campeau & Anand V. Sastry & Svetlana Maurya & Kevin Rychel & David J. Gonzalez & Bernhard O. Palsson, 2024. "Proteome allocation is linked to transcriptional regulation through a modularized transcriptome," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Olga Iwańska & Przemysław Latoch & Natalia Kopik & Mariia Kovalenko & Małgorzata Lichocka & Remigiusz Serwa & Agata L. Starosta, 2024. "Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Vincent Charron-Lamoureux & Lounès Haroune & Maude Pomerleau & Léo Hall & Frédéric Orban & Julie Leroux & Adrien Rizzi & Jean-Sébastien Bourassa & Nicolas Fontaine & Élodie V. d’Astous & Philippe Daup, 2023. "Pulcherriminic acid modulates iron availability and protects against oxidative stress during microbial interactions," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Donghui Choe & Connor A. Olson & Richard Szubin & Hannah Yang & Jaemin Sung & Adam M. Feist & Bernhard O. Palsson, 2024. "Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Cosme Claverie & Francesco Coppolino & Maria-Vittoria Mazzuoli & Cécile Guyonnet & Elise Jacquemet & Rachel Legendre & Odile Sismeiro & Giuseppe Valerio Gaetano & Giuseppe Teti & Patrick Trieu-Cuot & , 2024. "Constitutive activation of two-component systems reveals regulatory network interactions in Streptococcus agalactiae," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Yichao Han & Wanji Li & Alden Filko & Jingyao Li & Fuzhong Zhang, 2023. "Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli," Nature Communications, Nature, vol. 14(1), pages 1-13, 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_s41467-023-43173-7. 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.