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A ubiquitin-selective AAA-ATPase mediates transcriptional switching by remodelling a repressor–promoter DNA complex

Nature Cell Biology volume 11, pages 1481–1486 (2009)Cite this article

Abstract

Switches between different phenotypes and their underlying states of gene transcription occur as cells respond to intrinsic developmental cues or adapt to changing environmental conditions. Post-translational modification of the master regulatory transcription factors that define the initial phenotype is a common strategy to direct such transitions. Emerging evidence indicates that the modification of key transcription factors by the small polypeptide ubiquitin has a central role in many of these transitions1,2. However, the molecular mechanisms by which ubiquitylation regulates the switching of promoters between active and inactive states are largely unknown. Ubiquitylation of the yeast transcriptional repressor α2 is necessary to evoke the transition between mating-types3, and here we dissect the impact of this modification on α2 dynamics at its target promoters. Ubiquitylation of α2 does not alter DNA occupancy by depleting the existing pool of the transcription factor, despite its well-characterized function in directing repressor turnover. Rather, α2 ubiquitylation has a direct role in the rapid removal of the repressor from its DNA targets. This disassembly of α2 from DNA depends on the ubiquitin-selective AAA-ATPase Cdc48. Our findings expand the functional targets of Cdc48 to include active transcriptional regulatory complexes in the nucleus. These data reveal an ubiquitin-dependent extraction pathway for dismantling transcription factor–DNA complexes and provide an archetype for the regulation of transcriptional switching events by ubiquitylation.

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Figure 1: Increased expression of α2 does not affect its dissociation from DNA.
Figure 2: Overexpression of α2 leads to increased DNA-binding.
Figure 3: Cdc48 and the ubiquitylation machinery of α2 are actively involved in α2 dissociation from DNA.
Figure 4: α2 bound to its specific target sites is ubiquitylated.
Figure 5: The rapid dissociation of α2 from promoter DNA is required for the timely de-repression of an α2 target gene.

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Acknowledgements

We are grateful to Y. Xie and M. Hochstrasser for sharing data and reagents in advance of publication, for providing strains and plasmids and for many discussions. We thank R. Hampton and S. Jentsch for providing strains, R. Whitaker and R. Reenan for the sequencing of cdc48 alleles, J. Mead and D. Vershon for the His-tagged α2 construct, S. Gregory and A. Dahlberg for their help with the footprinting experiments, and T. Serio for numerous discussions. Our ideas were also shaped by discussions with K. Wilkinson and R. Deshaies. The manuscript was improved by comments from T. Serio, J. Bender, Y. Xie, M. Hochstrasser, R. Reenan and A. DeSimone. This work was supported by a grant from the National Institutes of Health (GM71764 to J.D.L.) and by a Basil O'Connor Starter Scholar Research Award from the March of Dimes.

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  1. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G-L2, Providence, 02912, RI, USA

    Alexander J. Wilcox & Jeffrey D. Laney

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A.J.W. performed all of the experiments. A.J.W. and J.D.L. conceived and designed the experiments, analysed the results and prepared the manuscript.

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Correspondence to Jeffrey D. Laney.

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Wilcox, A., Laney, J. A ubiquitin-selective AAA-ATPase mediates transcriptional switching by remodelling a repressor–promoter DNA complex. Nat Cell Biol 11, 1481–1486 (2009). https://doi.org/10.1038/ncb1997

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