Abstract
Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery plays a regulatory role in gene expression remained unclear. Here, we show that DNA indeed transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which allows a fine-tuning of the dynamic properties of genetic circuits.
Highlights
Allostery is a pervasive principle to regulate protein function
The resulting cooperativity regulates the activity of many proteins and molecular machines[6,7,8], but it is key for the behaviour of genetic circuits with binary[9], oscillatory[10], excitable[11,12], or pulsing[13] dynamics
Using single-molecule Förster resonance energy transfer and cryo-electron microscopy we show how ComK binding at one site enhances binding to a distant site via allosteric changes in DNA
Summary
Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that DNA is capable of transmitting allosteric signals. We show that DNA transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. We show that Bacillus subtilis bacteria utilize long-range allostery in a stochastic and reversible phenotype switch (Fig. 1a). The critical threshold acts like an analogueto-digital converter: the ComK target promoter is inactive at low concentrations, but it switches cooperatively to an active state within a narrow ComK concentration range (Fig. 1c)[11,12]. Using single-molecule Förster resonance energy transfer (smFRET) and cryo-electron microscopy (cryo-EM) we show how ComK binding at one site enhances binding to a distant site via allosteric changes in DNA
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