Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli.

Protein synthesis efficiency is highly dependent on the messenger RNA (mRNA) coding sequence. Furthermore, there is extensive evidence of a correlation between mRNA stability and protein expression level, though the mechanistic determinants remain unclear. Using yellow fluorescent protein (YFP) as a reporter gene, we herein demonstrate that adenosine (A) abundance in the first six codons is a critical determinant for achieving high protein synthesis in Escherichia coli. Increasing A and/or decreasing guanosine (G) content in this region with synonymous codons results in substantial increases in protein expression level both in vivo and in vitro that are correlated with steady-state mRNA concentration in vivo. The change in mRNA concentration is attributable to changes in the stability of the mRNA that are directly coupled to its translation efficiency. Increasing A content promotes mRNA incorporation into the functional 70S ribosomal initiation complex without altering its affinity for the 30S ribosomal subunit. These results support a model in which base composition in the first six codons modulates local mRNA folding energy and single-strandedness to control the balance between productive translation initiation versus degradation of mRNAs bound to the 30S ribosomal subunit. Based on these findings, we developed a short N-terminal coding sequence that optimizes translation initiation efficiency for protein production in E. coli.