A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch

Chem Biol. 2014 Feb 20;21(2):205-16. doi: 10.1016/j.chembiol.2013.11.012. Epub 2014 Jan 2.

Abstract

The tetrahydrofolate (THF) riboswitch regulates folate transport and metabolism in a number of Firmicutes by cooperatively binding two molecules of THF. To further understand this riboswitch's specificity for THF, binding and regulatory activity of a series of THF analogs and antifolates were examined. Our data reveal that although binding is dominated by the RNA's interactions with the pterin moiety, the para-aminobenzoic acid (pABA) moiety plays a significant role in transcriptional regulation. Further, we find that adenine and several other analogs bind with high affinity by an alternative binding mechanism. Despite a similar affinity to THF, adenine is a poor regulator of transcriptional attenuation. These results demonstrate that binding alone does not determine a compound's effectiveness in regulating the activity of the riboswitch-a complication in current efforts to develop antimicrobials that target these RNAs.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenine / chemistry
  • Adenine / metabolism
  • Binding Sites
  • Folic Acid Antagonists / chemistry
  • Folic Acid Antagonists / metabolism*
  • Leucovorin / chemistry
  • Leucovorin / metabolism
  • Methotrexate / chemistry
  • Methotrexate / metabolism
  • Molecular Docking Simulation
  • Nucleic Acid Conformation
  • Purines / chemistry
  • Purines / metabolism*
  • Riboswitch*
  • Tetrahydrofolates / chemistry
  • Tetrahydrofolates / metabolism*
  • Transcription Termination, Genetic

Substances

  • Folic Acid Antagonists
  • Purines
  • Riboswitch
  • Tetrahydrofolates
  • 5,6,7,8-tetrahydrofolic acid
  • Adenine
  • Leucovorin
  • Methotrexate