A New Model for Phenotypic Suppression of Frameshift Mutations by Mutant tRNAs

Abstract

According to the prevailing model, frameshift-suppressing tRNAs with an extra nucleotide in the anticodon loop suppress +1 frameshift mutations by recognizing a four-base codon and promoting quadruplet translocation. We present three sets of experiments that suggest a general alternative to this model. First, base modification should actually block such a four-base interaction by two classical frameshift suppressors. Second, for one Salmonella suppressor tRNA, it is not mutant tRNA but a structurally normal near cognate that causes the +1 shift in-frame. Finally, frameshifting occurs in competition with normal decoding of the next in-frame codon, consistent with an event that occurs in the ribosomal P site after the translocation step. These results suggest an alternative model involving peptidyl-tRNA slippage at the classical CCC-N and GGG-N frameshift suppression sites.

Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops

“…The remodeling of the P-site tRNA results in changes that are propagated to the codon-anticodon interaction, allowing a readjustment into the +1 frame. These data are consistent with and provide a new molecular basis for previously proposed repairing models, whereby mRNA-tRNA repairing is initiated by the ribosome gripping the ASL stem (30).…”

“…Despite these advances, very few structural studies have been able to provide a molecular understanding of mRNA frameshifting. Here, we investigated the structural basis for +1 decoding by a well-studied suppressor, tRNA SufA6 (17,30). Frameshift suppressor tRNA SufA6 is a derivative of tRNA Pro CGG and contains an inserted guanosine (G37.5) between positions 37 and 38 in the anticodon loop (Fig.…”

“…1A). tRNA SufA6 suppresses a mutagen-induced cytosine insertion in the Salmonella typhimurium histidine operon by decoding CCC-N codon as proline (where N represents any nucleotide) (17,30) (Fig. 1B).…”

“…This 4-nt decoding or +1 frameshifting event restores the correct reading frame and reverts a nonsense truncated protein back to the WT protein. The presence of an N1-methylation at position 37 (m 1 G37) in tRNA SufA6 precludes base pairing with the cytosinerich proline codon and thus, prevents a 4-base codon-anticodon interaction (30). We investigated both how tRNA SufA6 mediates frameshifting and what role the modification plays in mRNA frame maintenance by determining nine X-ray crystal structures of either the ASL SufA6 or ASL Pro bound to the Thermus thermophilus 70S A site at resolutions of 2.9-3.9 Å (Tables S1 and S2).…”

Evidence that the bypassing ribosome travels through the coding gap

“…This implied relationship between P-site pairing and A-site function might be another facet of the discovery by Farabaugh, Björk, and colleagues (24)(25)(26)(27)(28) that aberrant pairing in the P-site underlies frameshifting in a number of cases. Such aberrant pairing would be experienced by the bypassing peptidyl-tRNA from the time it disengages from the takeoff codon until it pairs with a cognate landing codon.…”