Table 1. Comparison of codon usage for E. coli in wild and optimized hEs gene based on Ikemura classification.
|
Codons
(Number) |
a E . coli Kazusa (%) | b E . coli high exp (%) |
Wt.hEs
(%) |
Opt.hEs
(%) |
Codons
(Number) |
a E . coli Kazusa (%) | b E . coli high exp. (%) | Wt.hEs (%) |
Opt.hEs
(%) |
| Ala (19) | - | - | - | - | Pro (10) | - | - | - | - |
| GCC | 23.87 | 16.14 | 57.89 | 0.00 | *CCC | 5.63 | 1.63 | 80 | 0 |
| GCG | 27.99 | 32.30 | 21.05 | 5.26 | CCG | 19.35 | 71.89 | 20 | 100 |
| GCT | 17.36 | 27.54 | 10.52 | 84.21 | Ser (20) | - | - | - | - |
| GCA | 21.60 | 24.01 | 10.52 | 10.52 | AGC | 15 | 24.33 | 40 | 0 |
| Arg (15) | - | - | - | - | *TCG | 8.52 | 7.39 | 20 | 0 |
| CGC | 18.38 | 32.97 | 37.5 | 0 | *TCC | 9.29 | 26.56 | 20 | 0 |
| *CGG | 6.49 | 0.80 | 20 | 0.00 | *TCA | 9.94 | 4.79 | 10 | 0 |
| *AGG | 2.56 | 0.29 | 20 | 0 | *TCT | 10.94 | 32.41 | 5 | 100 |
| CGT | 18.92 | 64.25 | 6.66 | 100 | *AGT | 10.73 | 4.52 | 5 | 0 |
| Asp (8) | - | - | - | - | Trp (4) | - | - | - | - |
| GAC | 18.83 | 46.05 | 100 | 12.5 | TGG | 13.78 | 100.00 | 100 | 100 |
| GAT | 32.38 | 53.95 | 0 | 87.5 | Val (9) | - | - | - | - |
| Asn (4) | - | - | - | - | GTG | 23.47 | 26.81 | 66.66 | 0 |
| AAC | 21.20 | 82.75 | 100 | 100 | GTC | 14.04 | 13.45 | 22.22 | 0 |
| Cys (4) | - | - | - | - | GTT | 20.04 | 39.77 | 11.11 | 100 |
| TGC | 5.99 | 61.15 | 75 | 100 | Lys (5) | - | - | - | - |
| TGT | 5.35 | 38.85 | 25 | 0 | AAG | 13.05 | 21.45 | 100 | 0 |
| Gly (16) | - | - | - | - | AAA | 35.60 | 78.55 | 0 | 100 |
| GGC | 25.66 | 42.83 | 56.25 | 0 | Thr (7) | - | - | - | - |
| *GGG | 11.58 | 4.36 | 37.5 | 0 | ACC | 21.39 | 53.60 | 42.86 | 100 |
| GGT | 24.93 | 50.84 | .6.25 | 93.75 | ACG | 13.76 | 12.65 | 42.86 | 0 |
| *GGA | 1.61 | 1.97 | 0 | 6.25 | ACT | 11.02 | 29.08 | 14.28 | 0 |
| Glu (7) | - | - | - | - | Phe (10) | - | - | - | - |
| GAG | 18.80 | 24.65 | 100 | 85.72 | TTC | 15.62 | 70.92 | 80 | 90 |
| GAA | 18.83 | 75.35 | 0 | 14.28 | TTT | 22.46 | 29.08 | 20 | 10 |
| Gln (8) | - | - | - | - | Ile (6) | - | - | - | - |
| CAG | 28.12 | 81.35 | 100 | 100 | ATC | 22.69 | 65.94 | 83.33 | 100 |
| Tyr (3) | - | - | - | - | ATT | 29.67 | 33.49 | 16.67 | 0 |
| TAC | 12.01 | 64.77 | 100 | 100 | Met (3) | - | - | - | - |
| Leu (20) | - | - | - | - | ATG | 25.95 | 100.00 | 100 | 100 |
| CTG | 46.4 | 76.67 | 75 | 100 | Stop | - | - | - | - |
| CTC | 10.08 | 8.03 | 25 | 0 | TAA | 1.99 | - | 0 | 50 |
| His (7) | - | - | - | - | TGA | 1.04 | - | 0 | 50 |
| CAC | 8.82 | 70.23 | 71.42 | 100 | TAG | 0.29 | - | 100 | 0 |
| CAT | 12.47 | 29.77 | 28.58 | 0 | GC% | - | - | 68% | 55% |
Codons with low frequency (<10%) are highlighted in yellow (light) and the most preferred codon for each amino acid is highlighted in gray (dark). The optimized hEs gene has lower preferred codons with low frequency than native gene. For gene optimization, rare codons frequency can cause translation error (3.94%) were set to 0.18 and the GC content reduced from 68 % to 55 %, closer to the average GC content of other highly expressed genes in E. coli.
aTaken and adapted from http://www.kazusa.or.jp/codon, bthegenes correspond to genes highly expressed during exponential growth and *Rare codon.