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Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli

Author

Listed:
  • Alla Gagarinova

    (University of Regina)

  • Ali Hosseinnia

    (University of Regina)

  • Matineh Rahmatbakhsh

    (University of Regina)

  • Zoe Istace

    (University of Regina)

  • Sadhna Phanse

    (University of Regina)

  • Mohamed Taha Moutaoufik

    (University of Regina)

  • Mara Zilocchi

    (University of Regina)

  • Qingzhou Zhang

    (University of Regina)

  • Hiroyuki Aoki

    (University of Regina)

  • Matthew Jessulat

    (University of Regina)

  • Sunyoung Kim

    (University of Regina)

  • Khaled A. Aly

    (University of Regina)

  • Mohan Babu

    (University of Regina)

Abstract

Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits.

Suggested Citation

  • Alla Gagarinova & Ali Hosseinnia & Matineh Rahmatbakhsh & Zoe Istace & Sadhna Phanse & Mohamed Taha Moutaoufik & Mara Zilocchi & Qingzhou Zhang & Hiroyuki Aoki & Matthew Jessulat & Sunyoung Kim & Khal, 2022. "Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31819-x
    DOI: 10.1038/s41467-022-31819-x
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    Cited by:

    1. Hai He & Paul A. Gómez-Coronado & Jan Zarzycki & Sebastian Barthel & Jörg Kahnt & Peter Claus & Moritz Klein & Melanie Klose & Valérie Crécy-Lagard & Daniel Schindler & Nicole Paczia & Timo Glatter & , 2024. "Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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