Beyond the paradigm of base readout: How do bacterial transcription factors recognize their DNA targets?

Specific recognition of DNA sites by transcription factors (TFs) is central to the regulation of gene expression, but the molecular mechanisms underlying protein–DNA recognition remain incompletely understood.

While it is established that eukaryotic TFs commonly employ DNA shape readout, use of this recognition mechanism by prokaryotic TFs has largely been overlooked.

However, we have recently shown that the iron-dependent regulator IdeR from the erythromycin producer Saccharopolyspora erythraea uses shape readout, identifying its targets by their sequence-dependent structure rather than through contacts with DNA bases.

Here we will use IdeR as a model system to fill in the gaps in our understanding of this recognition mechanism, addressing two main questions: (1) How does IdeR read DNA shape? (2) How does IdeR regulate genes with different target sites? The applicant will be active in this project at 50%. A PhD student will address question 1.

Two postdocs (2-years each) will investigate question 2.

Using X-ray crystallography, cryo-EM and NMR in conjunction with mutagenesis and DNA-binding assays, we will reveal which DNA shapes IdeR recognizes and how it deforms the DNA upon binding.

RNA sequencing and reporter genes will be used to establish the link between the pattern recognition flexibility of IdeR observed in vitro and the resulting gene expression profile in vivo, and will also reveal how IdeR influences production of erythromycin and other secondary metabolites.