rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift.
Base pairing between the 3' end of 16S rRNA and mRNA is shown to be important for the programmed -1 frameshifting utilized in decoding the Escherichia coli dnaX gene. This pairing is the same as the Shine-Dalgarno pairing used by prokaryotic ribosomes in selection of translation initiators, but for frameshifting the interaction occurs within elongating ribosomes. For dnaX -1 frameshifting, the 3' base of the Shine-Dalgarno sequence is 10 nucleotides 5' of the shift site. Previously, Shine-Dalgarno rRNA-mRNA pairing was shown to stimulate the +1 frameshifting necessary for decoding the release factor 2 gene. However, in the release factor 2 gene, the Shine-Dalgarno sequence is located 3 nucleotides 5' of the shift site. When the Shine-Dalgarno sequence is moved to the same position relative to the dnaX shift site, it is inhibitory rather than stimulatory. Shine-Dalgarno interactions by elongating ribosomes are likely to be used in stimulating -1 frameshifting in the decoding of a variety of genes.
Larsen
B
B
Howard Hughes Medical Institute, University of Utah, Salt Lake City 84112.
Wills
N M
NM
Gesteland
R F
RF
Atkins
J F
JF
D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D004252:DNA Mutational Analysis; D004258:DNA Polymerase III / Q000096:biosynthesis / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000096:biosynthesis / Q000235:genetics*; D014176:Protein Biosynthesis; D012330:RNA, Double-Stranded / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis; D017384:Sequence Deletion; D013329:Structure-Activity Relationship
D010454:Peptide Termination Factors; D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D011993:Recombinant Fusion Proteins; C041460:peptide chain termination release factor 2; D004258:DNA Polymerase III