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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

Author

Listed:
  • Kevin Rychel

    (University of California San Diego)

  • Anand V. Sastry

    (University of California San Diego)

  • Bernhard O. Palsson

    (University of California San Diego
    University of California San Diego
    Novo Nordisk Foundation Center for Biosustainability)

Abstract

The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover putative or recently discovered roles for at least five regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20153-9
    DOI: 10.1038/s41467-020-20153-9
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    Cited by:

    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. 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.
    3. 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.
    4. 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.

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