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Structural insights into CodY activation and DNA recognition.

Tobias Hainzl1,2, Mari Bonde1,3, Fredrik Almqvist1,2

  • 1Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.

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Structural insights reveal how CodY, a key regulator in Staphylococcus aureus and Enterococcus faecalis, binds DNA and integrates metabolism with virulence factor expression, aiding pathogen infection.

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Area of Science:

  • Microbiology
  • Structural Biology
  • Molecular Biology

Background:

  • Virulence factors are crucial for bacterial pathogens like Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef) to cause disease.
  • The pleiotropic transcription factor CodY integrates metabolic status with virulence gene expression in these Gram-positive pathogens.
  • The structural basis for CodY's activation and DNA binding mechanism remained largely unknown.

Purpose of the Study:

  • To elucidate the structural mechanisms of CodY activation and DNA recognition in Staphylococcus aureus and Enterococcus faecalis.
  • To understand how CodY integrates metabolic signals with virulence factor expression.

Main Methods:

  • X-ray crystallography was used to determine the structures of CodY from Sa and Ef in ligand-free and ligand-bound states, including complexed with DNA.
  • Biochemical assays were employed to validate the findings.

Main Results:

  • Crystal structures revealed ligand binding (branched-chain amino acids and GTP) induces conformational changes in CodY, affecting its DNA-binding domains.
  • CodY utilizes a non-canonical DNA recognition mechanism based on DNA shape readout.
  • Two CodY dimers bind cooperatively to overlapping DNA sites, involving cross-dimer interactions and minor groove deformation.

Conclusions:

  • The study provides a structural and biochemical explanation for CodY's ability to bind diverse substrates, characteristic of pleiotropic regulators.
  • These findings enhance our understanding of virulence activation mechanisms in significant human bacterial pathogens.