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Divergence in a eukaryotic transcription factor’s co-TF dependence involves multiple intrinsically disordered regions

Author

Listed:
  • Lindsey F. Snyder

    (University of Iowa)

  • Emily M. O’Brien

    (University of Iowa)

  • Jia Zhao

    (University of Iowa
    Massachusetts Institute of Technology)

  • Jinye Liang

    (University of Iowa)

  • Baylee J. Bruce

    (University of Iowa)

  • Yuning Zhang

    (Duke University
    Washington University School of Medicine)

  • Wei Zhu

    (Duke University)

  • Thomas H. Cassier

    (University of Iowa)

  • Nicholas J. Schnicker

    (University of Iowa
    University of Iowa)

  • Xu Zhou

    (Boston Children’s Hospital and Harvard Medical School)

  • Raluca Gordân

    (Duke University
    Duke University
    Duke University
    Duke University)

  • Bin Z. He

    (University of Iowa
    University of Iowa)

Abstract

Combinatorial control by transcription factors (TFs) is central to eukaryotic gene regulation, yet its mechanism, evolution, and regulatory impact are not well understood. Here we use natural variation in the yeast phosphate starvation (PHO) response to examine the genetic basis and species variation in TF interdependence. In Saccharomyces cerevisiae, the main TF Pho4 relies on the co-TF Pho2 to regulate ~28 genes, whereas in the related pathogen Candida glabrata, Pho4 has reduced Pho2 dependence and regulates ~70 genes. We found C. glabrata Pho4 (CgPho4) binds the same motif with 3–4 fold higher affinity. Machine learning and yeast one-hybrid assay identify two intrinsically disordered regions (IDRs) in CgPho4 that boost its activation domain’s activity. In ScPho4, an IDR next to the DNA binding domain both allows for enhanced activity with Pho2 and inhibits activity without Pho2. This study reveals how IDR divergence drives TF interdependence evolution by influencing activation potential and autoinhibition.

Suggested Citation

  • Lindsey F. Snyder & Emily M. O’Brien & Jia Zhao & Jinye Liang & Baylee J. Bruce & Yuning Zhang & Wei Zhu & Thomas H. Cassier & Nicholas J. Schnicker & Xu Zhou & Raluca Gordân & Bin Z. He, 2025. "Divergence in a eukaryotic transcription factor’s co-TF dependence involves multiple intrinsically disordered regions," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59244-w
    DOI: 10.1038/s41467-025-59244-w
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    References listed on IDEAS

    as
    1. Vincent J. Lynch & Gemma May & Günter P. Wagner, 2011. "Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB," Nature, Nature, vol. 480(7377), pages 383-386, December.
    2. Felix H. Lam & David J. Steger & Erin K. O’Shea, 2008. "Chromatin decouples promoter threshold from dynamic range," Nature, Nature, vol. 453(7192), pages 246-250, May.
    3. Annie E. Tsong & Brian B. Tuch & Hao Li & Alexander D. Johnson, 2006. "Evolution of alternative transcriptional circuits with identical logic," Nature, Nature, vol. 443(7110), pages 415-420, September.
    Full references (including those not matched with items on IDEAS)

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