Specific protection of 16 S rRNA by translational initiation factors

J Mol Biol. 1995 Apr 28;248(2):207-10. doi: 10.1016/s0022-2836(95)80042-5.


The binding of initiation factors to 30 S ribosomal subunits protects specific sets of nucleotides in 16 S rRNA from base-specific chemical probes. Initiation factor 3 (IF-3) protects residues G700, G703 and G791 from attack by kethoxal. These protected bases are close to those in 16 S rRNA that are protected by 50 S subunits, providing a structural basis for the subunit dissociation activity of IF-3. The IF-3-dependent protections also flank bases that are protected by P-site-bound tRNA, in keeping with the possibility that IF-3 may interact with initiator tRNA, or influence the properties of the 30 S P site during initiation. IF-1 protects G530, A1492 and A1493 and causes enhanced reactivity of A1408. These bases are precisely the ones that are protected by the binding of tRNA to the ribosomal A site. This suggests that IF-1 mimics A-site-bound tRNA, and could serve to prevent premature binding of aminoacyl tRNA by blocking the 30 S A site. We were unable to detect any effect of IF-2 on the reactivity pattern of 16 S rRNA, suggesting that this factor may interact primarily through protein-protein interactions.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Aldehydes / pharmacology
  • Bacterial Proteins / metabolism*
  • Butanones
  • Escherichia coli / metabolism*
  • Eukaryotic Initiation Factor-1 / metabolism
  • Molecular Probes
  • Peptide Initiation Factors / metabolism*
  • Prokaryotic Initiation Factor-1
  • Prokaryotic Initiation Factor-3
  • Protein Binding
  • RNA, Ribosomal, 16S / drug effects
  • RNA, Ribosomal, 16S / metabolism*
  • RNA, Transfer / metabolism


  • Aldehydes
  • Bacterial Proteins
  • Butanones
  • Eukaryotic Initiation Factor-1
  • Molecular Probes
  • Peptide Initiation Factors
  • Prokaryotic Initiation Factor-1
  • Prokaryotic Initiation Factor-3
  • RNA, Ribosomal, 16S
  • RNA, Transfer
  • kethoxal