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Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

Nature volume 480, pages 383–386 (2011)Cite this article

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A Corrigendum to this article was published on 16 April 2014

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Abstract

There is an emerging consensus that gene regulation evolves through changes in cis-regulatory elements1,2 and transcription factors3,4,5,6. Although it is clear how nucleotide substitutions in cis-regulatory elements affect gene expression, it is not clear how amino-acid substitutions in transcription factors influence gene regulation4,5,6,7,8,9,10. Here we show that amino-acid changes in the transcription factor CCAAT/enhancer binding protein-β (CEBPB, also known as C/EBP-β) in the stem-lineage of placental mammals changed the way it responds to cyclic AMP/protein kinase A (cAMP/PKA) signalling. By functionally analysing resurrected ancestral proteins, we identify three amino-acid substitutions in an internal regulatory domain of CEBPB that are responsible for the novel function. These amino-acid substitutions reorganize the location of key phosphorylation sites, introducing a new site and removing two ancestral sites, reversing the response of CEBPB to GSK-3β-mediated phosphorylation from repression to activation. We conclude that changing the response of transcription factors to signalling pathways can be an important mechanism of gene regulatory evolution.

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Figure 1: CEBPB cooperatively regulates gene expression with FOXO1A in placental mammals.
Figure 2: CEBPB evolved a novel GSK-3B phosphorylation site in an internal regulatory domain.
Figure 3: Phosphorylation induces a conformation change in CEBPB.

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Acknowledgements

This work was funded by a grant from the John Templeton Foundation, number 12793 Genetics and the Origin of Organismal Complexity; results presented here do not necessarily reflect the views of the John Templeton Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Authors and Affiliations

  1. Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, 06511, Connecticut, USA

    Vincent J. Lynch, Gemma May & Günter P. Wagner

Authors
  1. Vincent J. Lynch
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  2. Gemma May
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  3. Günter P. Wagner
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Contributions

V.J.L. and G.P.W. designed experiments and wrote the manuscript. V.J.L. performed experiments and analysed data. G.M. cloned and sequenced CEBPB genes from non-mammalian species.

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Correspondence to Vincent J. Lynch.

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The authors declare no competing financial interests.

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Lynch, V., May, G. & Wagner, G. Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB. Nature 480, 383–386 (2011). https://doi.org/10.1038/nature10595

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