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Evolution of alternative transcriptional circuits with identical logic

Author

Listed:
  • Annie E. Tsong

    (Department of Biochemistry & Biophysics
    University of California San Francisco
    Immunology, University of California San Francisco
    University of California Berkeley, Lawrence Berkeley National Labs)

  • Brian B. Tuch

    (Department of Biochemistry & Biophysics
    University of California San Francisco
    Immunology, University of California San Francisco)

  • Hao Li

    (Department of Biochemistry & Biophysics)

  • Alexander D. Johnson

    (Department of Biochemistry & Biophysics
    University of California San Francisco
    Immunology, University of California San Francisco)

Abstract

Evolution of gene regulation is an important contributor to the variety of life. Here, we analyse the evolution of a combinatorial transcriptional circuit composed of sequence-specific DNA-binding proteins that are conserved among all eukaryotes. This circuit regulates mating in the ascomycete yeast lineage. We first identify a group of mating genes that was transcriptionally regulated by an activator in a fungal ancestor, but is now transcriptionally regulated by a repressor in modern bakers' yeast. Despite this change in regulatory mechanism, the logical output of the overall circuit remains the same. By examining the regulation of mating in modern yeasts that are related to different extents, we deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation. These changes indicate specific mechanisms by which fitness barriers were traversed during the transition.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:nature:v:443:y:2006:i:7110:d:10.1038_nature05099
    DOI: 10.1038/nature05099
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    Cited by:

    1. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Karel Janko & Jan Eisner & Petr Cigler & Tomáš Tichopád, 2024. "Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Iksoo Huh & Isabel Mendizabal & Taesung Park & Soojin V Yi, 2018. "Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals," PLOS Computational Biology, Public Library of Science, vol. 14(10), pages 1-21, October.
    4. Krishnan, Arun & Tomita, Masaru & Giuliani, Alessandro, 2008. "Evolution of gene regulatory networks: Robustness as an emergent property of evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(8), pages 2170-2186.
    5. Andreas Wagner, 2015. "Causal Drift, Robust Signaling, and Complex Disease," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-29, March.

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