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An intrinsically disordered entropic switch determines allostery in Phd–Doc regulation

Abstract

Conditional cooperativity is a common mechanism involved in transcriptional regulation of prokaryotic type II toxin–antitoxin operons and is intricately related to bacterial persistence. It allows the toxin component of a toxin–antitoxin module to act as a co-repressor at low doses of toxin as compared to antitoxin. When toxin level exceeds a certain threshold, however, the toxin becomes a de-repressor. Most antitoxins contain an intrinsically disordered region (IDR) that typically is involved in toxin neutralization and repressor complex formation. To address how the antitoxin IDR is involved in transcription regulation, we studied the phddoc operon from bacteriophage P1. We provide evidence that the IDR of Phd provides an entropic barrier precluding full operon repression in the absence of Doc. Binding of Doc results in a cooperativity switch and consequent strong operon repression, enabling context-specific modulation of the regulatory process. Variations of this theme are likely to be a common mechanism in the autoregulation of bacterial operons that involve intrinsically disordered regions.

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Figure 1: X-ray structure of Phd bound to the operator box 1 (Oln1).
Figure 2: Phd–Oln1 binding interface.
Figure 3: Energetics of the allosteric mechanism of autorepression of the phddoc operon.
Figure 4: Structural bases of the allosteric regulation of transcription of the phddoc operon.
Figure 5: Molecular model for the general mechanism of conditional cooperative regulation of the phddoc operon.
Figure 6: Regulation of the phddoc operon.

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Acknowledgements

The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under BioStruct-X (grant agreement no. 283570) and from the VIB, FWO-Vlaanderen, the Hercules Foundation, the Fonds National de Recherche Scientifique (FNRS) and the Fonds d'Encouragement à la Recherche ULB (FER-ULB). S.D.G. and A.G.-P. acknowledge the receipt of individual predoctoral and postdoctoral fellowships, respectively, from FWO-Vlaanderen. We also acknowledge the use of beamtime at the synchrotron beamlines BM29 (ESRF Grenoble, France) and SWING and PROXIMA1 (Soleil Gif-sur-Yvette, France) and thank the beamline staff for their support.

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Contributions

A.G.-P. performed the calorimetry experiments; collected and analyzed crystallographic, SAXS and EM data; and wrote the paper and supervised the project. S.D.G. purified Doc and Phd, prepared the Phd–Oln1 crystals and collected SAXS data. A.T. ran and analyzed the MD simulations. H.D.G. prepared the Phd mutants. R.G.E. collected and analyzed EM data and calculated EM models. R.L. wrote the paper and supervised the project.

Corresponding authors

Correspondence to Abel Garcia-Pino or Remy Loris.

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The authors declare no competing financial interests.

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Garcia-Pino, A., De Gieter, S., Talavera, A. et al. An intrinsically disordered entropic switch determines allostery in Phd–Doc regulation. Nat Chem Biol 12, 490–496 (2016). https://doi.org/10.1038/nchembio.2078

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