Table 2 Summary of literature references comparing protein expression levels for native and optimized DNAs in bacterial systems
From: Assessing optimal: inequalities in codon optimization algorithms
| First author | Optimization algorithma (source) | Target(s) | Number of constructs | Conclusions |
|---|---|---|---|---|
| Burgess-Brown [40] | Proprietary (Genscript, Sigma, and MediGene) | Various | 30 | • 26% of targets show higher expression of soluble protein for optimized over native CDS in E. coli |
| Kudla [27] | CAI | GFP | 154 |
• Fluorescence levels span > 1000-fold across different CDSs • No correlation between fluorescence levels and CAI • Modest relationship between mRNA 2° structure and GFP fluorescence |
| Welch [28] | PLSR (DNA 2.0) | φ29 DNA polymerase | 21 | • > 100-fold difference in protein yield observed by differently optimized DNAs |
| Maertens [41] | CAI (GeneArt) | Various | 100 |
• 24% targets showed ≥ 2× yield for optimized CDS • 20% targets showed lower expression for optimized CDS |
| Spencer [42] | Undefined | Firefly Luciferase | 7 |
• Optimization increased translation speeds ~ 2× with proportional decrease in functional protein • 2–2.5× yield and solubility increase when recoded for frequent codons in Drosophila melanogaster |
| Trösemeier [43] | CAI (GeneArt) COSEM |
ova manA |
5 11 |
• COSEM optimized sequences expressed ≥ 2× the native sequence • “Ramp” inclusion was necessary for significant boost in protein expression |
| Konczal [44] | CAI (GeneWiz) |
KRas4B RalA Rac1 |
11 11 11 | • “Deoptimization” with ≤ 4 rare codons improves solubility ≥ 4× compared to native CDS |