Fe2+ binds iron responsive element-RNA, selectively changing protein-binding affinities and regulating mRNA repression and activation

Proc Natl Acad Sci U S A. 2012 May 29;109(22):8417-22. doi: 10.1073/pnas.1120045109. Epub 2012 May 14.

Abstract

Iron increases synthesis rates of proteins encoded in iron-responsive element (IRE)-mRNAs; metabolic iron ("free," "labile") is Fe(2+). The noncoding IRE-RNA structure, approximately 30 nt, folds into a stem loop to control synthesis of proteins in iron trafficking, cell cycling, and nervous system function. IRE-RNA riboregulators bind specifically to iron-regulatory proteins (IRP) proteins, inhibiting ribosome binding. Deletion of the IRE-RNA from an mRNA decreases both IRP binding and IRP-independent protein synthesis, indicating effects of other "factors." Current models of IRE-mRNA regulation, emphasizing iron-dependent degradation/modification of IRP, lack answers about how iron increases IRE-RNA/IRP protein dissociation or how IRE-RNA, after IRP dissociation, influences protein synthesis rates. However, we observed Fe(2+) (anaerobic) or Mn(2+) selectively increase the IRE-RNA/IRP K(D). Here we show: (i) Fe(2+) binds to the IRE-RNA, altering its conformation (by 2-aminopurine fluorescence and ethidium bromide displacement); (ii) metal ions increase translation of IRE-mRNA in vitro; (iii) eukaryotic initiation factor (eIF)4F binds specifically with high affinity to IRE-RNA; (iv) Fe(2+) increased eIF4F/IRE-RNA binding, which outcompetes IRP binding; (v) exogenous eIF4F rescued metal-dependent IRE-RNA translation in eIF4F-depeleted extracts. The regulation by metabolic iron binding to IRE-RNA to decrease inhibitor protein (IRP) binding and increase activator protein (eIF4F) binding identifies IRE-RNA as a riboregulator.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 2-Aminopurine / chemistry
  • Base Sequence
  • Binding Sites
  • Ethidium / chemistry
  • Eukaryotic Initiation Factor-4F / chemistry
  • Eukaryotic Initiation Factor-4F / metabolism
  • Gene Expression Regulation*
  • Iron / chemistry
  • Iron / metabolism*
  • Iron-Regulatory Proteins / chemistry
  • Iron-Regulatory Proteins / metabolism*
  • Models, Genetic
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Response Elements*

Substances

  • Eukaryotic Initiation Factor-4F
  • Iron-Regulatory Proteins
  • RNA, Messenger
  • 2-Aminopurine
  • RNA
  • Iron
  • Ethidium