Many methods for improving recombinant protein expression in a heterologous host redesign the gene sequence. They aim to optimize translation initiation and to remove obstacles to elongation, such as mRNA secondary structure or codons that are rare in the host (1).
A widely used method replaces most infrequent codons with frequent synonymous ones to raise the codon adaptation index (CAI) (2), on the assumption that a high CAI predicts high expression (3). In practice this often gives low expression or insoluble aggregates, and protein that does stay soluble is not necessarily natively folded.
Studies published between 2009 and 2016 show that synonymous codons, rare ones in particular, affect protein expression, export (secretion) and co-translational folding (4–6).
DAPCEL™ RC (Rare Codon) gene optimization is a two-layered redesign strategy that takes rare codons and the overall kinetics of translation into account, with the aim of producing high yields of correctly folded, soluble protein. Synonymous codons leave the amino-acid sequence unchanged; expression, solubility and activity are what each project then tests.
Expression hosts. The approach can be adapted to different hosts. Its published results to date are in E. coli, including the 1369-amino-acid human DHX29 (see Publications). For other hosts, we discuss the expected improvement and its limits for your construct before work begins.
References:
1. Sørensen, H.P. and Mortensen, K.K. (2005) J. Biotechnol. 115, 113-128.
2. Sharp, P.M. and Li, W.H. (1987) Nucleic Acids Res. 15, 1281-1295.
3. Gustafsson, C., Govindarajan, S. and Minshull, J. (2004) Trends Biotechnol. 7, 346-353.
4. Komar, A.A. (2009) Trends Biochem Sci. 34, 16-24.
5. Zalucki, Y.M., Beacham, I.R. and Jennings, M.P. (2009) Trends Microbiol. 17, 146-150.
6. Komar, A.A. (2016) Top Med Chem, 2, 1-17.