title: Specific protection of 16 S rRNA by translational initiation factors.
abstract: 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.
authors.affiliation: Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA.
authors.forename: D
authors.initials: D
authors.lastname: Moazed
authors.forename: R R
authors.initials: RR
authors.lastname: Samaha
authors.forename: C
authors.initials: C
authors.lastname: Gualerzi
authors.forename: H F
authors.initials: HF
authors.lastname: Noller
mesh_terms: D000447:Aldehydes / Q000494:pharmacology; D001426:Bacterial Proteins / Q000378:metabolism*; D002074:Butanones; D004926:Escherichia coli / Q000378:metabolism*; D015977:Eukaryotic Initiation Factor-1 / Q000378:metabolism; D015335:Molecular Probes; D010448:Peptide Initiation Factors / Q000378:metabolism*; D039861:Prokaryotic Initiation Factor-1; D039665:Prokaryotic Initiation Factor-3; D011485:Protein Binding; D012336:RNA, Ribosomal, 16S / Q000187:drug effects / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism
chemical_list: D000447:Aldehydes; D001426:Bacterial Proteins; D002074:Butanones; D015977:Eukaryotic Initiation Factor-1; D015335:Molecular Probes; D010448:Peptide Initiation Factors; D039861:Prokaryotic Initiation Factor-1; D039665:Prokaryotic Initiation Factor-3; D012336:RNA, Ribosomal, 16S; D012343:RNA, Transfer; C005135:kethoxal