5′‐Secondary structure formation, in constrast to a short string of non‐preferred codons, inhibits the translation of the pyruvate kinase mRNA in yeast

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Abstract
The effects of poor codon bias and secondary structure formation upon the translation of the pyruvate kinase (PYK1) mRNA have been investigated in Saccharomyces cerevisiae. Following insertion mutagenesis at the 5′‐end of the PYK1 coding region, the gene was transformed into yeast, and translation assessed directly in vivo by determining the distribution of the modified PYK1 mRNAs across polysomes fractionated by sucrose density gradient centrifugation. The chromosomally‐encoded (wild‐type) PYK1 mRNA, and the actin, ribosomal protein L3 and glyceraldehyde‐3‐phosphate dehydrogenase mRNAs were used to control for minor differences between polysome preparations. An insertion containing 13 non‐preferred codons at the 5′‐end of the coding region was found to have no significant effect upon PYK1 mRNA translation. In contrast, translation was inhibited by an insertion which increased the formation of secondary structures at the 5′‐end of the mRNA (overall ΔG = −36·6 kcal/mol). Control insertions were also analysed to exclude the possibility that alterations to the amino acid sequence of pyruvate kinase affect the translation of its mRNA. These insertions, which introduced preferred codons or restored wild‐type levels of secondary structure formation, did not significantly influence PYK1 mRNA translation.