Modulating protein translation through proposed mRNA-rRNA base pairing

<p>Ribosomes are macromolecular assemblies consisting of roughly 80 proteins and three to four structural rRNAs and are responsible for translating mRNA sequences transcribed from the genomes of every known organism. Recent advances in constructing atomic-resolution structures of ribosomes and in their functional characterization at a genomic scale have mandated a more sophisticated description of the translational mechanism and its points of modulation. mRNA sequences have an inherent three-nucleotide periodicity marked by overrepresentation of a (GCN)_n repeating motif and an underrepresentation of guanine at the second position of codons. This periodicity is present in open reading frames but is absent in reading frames not utilized by the ribosome<em> in vivo</em>. Its magnitude is also correlated with high protein expression, further indicating its functional significance in translation. However, direct evidence for the effects of altering conformance to this sequence pattern is lacking. Here, alterations to this pattern are tested by probing gene expression at the protein and mRNA level in several mutants in two candidate genes in <em>Saccharomyces cerevisiae</em>. Greater conformance to (GCN)_n was found to significantly depress translation, whereas disrupting conformance had neutral or positive effects on translation. We then integrate these observations with bioinformatics analyses to develop a model for modulating translation through proposed mRNA base-pairing to the universally-conserved 530 loop in the small subunit rRNA. Such a model may help to explain differential translational regulation of gene subsets under stress, as well as slower decoding rates of initial codons.</p>