An mRNA‐rRNA Base Pairing Model for Efficient Protein Translation

Abstract

The idea that base pairing between mRNAs and structural rRNAs of ribosomes might contribute to protein translation has long been an intriguing possibility. The 530 loop of 16S rRNA has been implicated in translation initiation, elongation and termination. This loop and the corresponding highly‐conserved loop in 18S rRNA are located in the mRNA entrance tunnel of ribosomes. As noted before high‐resolution ribosome structures were described, the 530 loop contains a 3‐nucleotide‐repeating pattern complementary to the 3‐nucleotide periodicity of protein open reading frames characterized by overrepresentation of (GCN)n. We find that the 3‐nucleotide periodicity is significantly enhanced downstream of translation start codons of highly expressed Saccharomyces cerevisiae genes with significant depression of G at nucleotides 2 and 3 of these codons. We propose that during translocation steps, exposed rRNA nucleotides of the 530 loop can transiently base pair with the second and third mRNA nucleotides of the incoming A‐site codon before engagement of the A‐site tRNA and that this promotes efficient launching of the ribosome through the start region codons permitting high protein expression. This cooperation between the A‐site and 530 loop requires a precise positioning of the mRNA reading frame, which if compromised in several adjacent codons leads to low translation levels.Support or Funding InformationNational Institutes of Health 1R15GM096228Beckman Scholars Program, Arnold & Mabel Beckman FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.