Changes of Rare Codon and mRNA Structure Accelerate Expression of qa-3 in Escherichia coli

The key and crucial step of metabolic engineering during quinic acid biosynthesis using shikimic acid pathway is a high expression of quinate 5-dehydrogenase. The gene qa-3 which encoded quinate 5-dehydrogenase from Neurospora crassa wasn't expressed in Escherichia coli. In contrast with codon usage in Escherichia coli, there are 27 rare codons in qa-3, including eight AGG/AGA (Arg) and nine GGG (Gly). Two AGG are joined together (called box R) and some GGG codons are relatively concentrated (called box G). Along with the secondary structure of mRNA analyzed in computer, the free energy of mRNA changes a lot from −374.3 kJ/mol to −80.5 kJ/mol when some bases in the end of qa-3 were transformed, and moreover, the change of free energy is quite small when some bases in the box G and box R are transformed. Subsequent to the change of rare codon and optimization of some bases in the end, qa-3 was expressed in E. coli and also the enzyme activity of quinate 5-dehydrogenase could be accurately surveyed. All the above-mentioned work benefits further research on producing quinic acid engineering bacterium.