Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process

While eukaryotic ribosomes are widely presumed to scan mRNA for the AUG codon to initiate translation in a strictly 5'->3' movement (strictly unidirectional scanning model), other evidence has suggested that the ribosome uses small-amplitude 5'->3' and 3'->5' oscillations with a net 5'->3' movement to recognize the AUG codon (Brownian ratchet scanning model). Here, we generated 13,437 yeast variants, each with an ATG triplet placed downstream (dATGs) of the annotated ATG (aATG) codon of green fluorescent protein. We found that out-of-frame dATGs could inhibit translation at the aATG, but with diminishing strength over increasing distance between aATG and dATG, undetectable beyond ~17 nt. Computational simulations revealed that each triplet is scanned back and forth approximately ~10 times until an AUG codon is recognized. Collectively, our findings uncover the basic process by which eukaryotic ribosomes scan for initiation codons, and how this process could shape eukaryotic genome evolution and influence cancer development.