TABLE 5.
T4 and E. coli codon usage and tRNA availability
| Amino acid | Codon usagea
|
tRNA availability, gene copy no. [relative content]b
|
||||
|---|---|---|---|---|---|---|
| Codon | Cumulative frequency (per 103)
|
Anticodon | ||||
| E. coli | T4 | E. coli | T4 | |||
| Arg | CGU | 20.9 | 19.1 | ACG | 4 [0.9] | |
| CGC | 22.0 | 5.7 | ||||
| CGA | 3.6 | 5.6 | ||||
| CGG | 5.4 | 1.1 | CCG | 1 [minor] | ||
| AGA | 2.1 | 9.9 | UCU | 1 [minor] | 1 | |
| AGG | 1.2 | 1.8 | CCU | 1 [minor] | ||
| Leu | UUA | 13.9 | 27.8 | UAA | 1 [0.25] | 1 |
| UUG | 13.7 | 10.7 | CAA | 1 [0.2] | ||
| CUU | 11.0 | 18.3 | ||||
| CUC | 11.1 | 4.1 | GAG | 1 [0.3] | ||
| CUA | 3.9 | 7.0 | UAG | 1 [minor] | ||
| CUG | 52.6 | 5.6 | CAG | 4 [1.0] | ||
| Ser | UCU | 8.5 | 24.7 | |||
| UCC | 8.6 | 3.6 | GGA | 2 [0.25] | ||
| UCA | 7.2 | 18.4 | UGA | 1 [0.25] | 1 | |
| UCG | 8.9 | 3.8 | CGA | 1 [0.05] | ||
| AGU | 8.8 | 10.5 | ||||
| AGC | 16.1 | 5.6 | GCU | 1 [0.25] | ||
| Ala | GCU | 15.3 | 31.1 | |||
| GCC | 25.5 | 5.2 | GGC | 2 [0.3] | ||
| GCA | 20.1 | 19.6 | UGC | 3 [1.0] | ||
| GCG | 33.6 | 6.5 | ||||
| Gly | GGU | 24.7 | 27.7 | |||
| GGC | 29.6 | 8.1 | GCC | 4 [1.1] | ||
| GGA | 8.0 | 19.5 | UCC | 1 [0.15] | 1 | |
| GGG | 11.1 | 3.9 | CCC | 1 [0.1] | ||
| Pro | CCU | 7.0 | 14.3 | |||
| CCC | 5.5 | 1.1 | GGG | 1 [minor] | ||
| CCA | 8.4 | 13.9 | UGG | 1 [0.3] | 1 | |
| CCG | 23.2 | 4.8 | CGG | 1 [0.3] | ||
| Thr | ACU | 9.0 | 27.9 | |||
| ACC | 23.4 | 6.3 | GGU | 2 [0.8] | ||
| ACA | 7.1 | 16.8 | UGU | 1 [0.1] | 1 | |
| ACG | 14.4 | 5.4 | CGU | 2 [0.1] | ||
| Val | GUU | 18.3 | 31.6 | |||
| GUC | 15.3 | 5.4 | GAC | 2 [0.4] | ||
| GUA | 10.9 | 20.1 | UAC | 5 [1.05] | ||
| GUG | 26.4 | 6.2 | ||||
| Ile | AUU | 30.3 | 51.3 | |||
| AUC | 25.1 | 11.2 | GAU | 3 [1.0] | ||
| AUA | 4.4 | 12.0 | CAU | 2 [0.05] | 1 | |
| Asn | AAU | 17.7 | 42.3 | |||
| AAC | 21.7 | 14.8 | GUU | 4 [0.6] | ||
| Asp | GAU | 32.1 | 47.4 | |||
| GAC | 19.1 | 14.8 | GUC | 3 [0.8] | ||
| Cys | UGU | 5.2 | 7.3 | |||
| UGC | 6.5 | 3.8 | GCA | 1 [minor] | ||
| Gln | CAA | 15.3 | 21.9 | UUG | 2 [0.3] | 1 |
| CAG | 28.8 | 11.1 | CUG | 2 [0.4] | ||
| Glu | GAA | 39.4 | 60.0 | UUC | 4 [0.9] | |
| GAG | 17.8 | 10.8 | ||||
| His | CAU | 12.9 | 13.7 | |||
| CAC | 9.7 | 4.0 | GUG | 1 [0.4] | ||
| Lys | AAA | 33.6 | 63.5 | UUU | 6 [1.0] | |
| AAG | 10.3 | 17.3 | ||||
| Phe | UUU | 22.3 | 33.4 | |||
| UUC | 16.6 | 11.1 | GAA | 2 [0.35] | ||
| Tyr | UAU | 16.2 | 33.7 | |||
| UAC | 12.2 | 9.7 | GUA | 3 [0.5] | ||
| Met | AUG | 27.9 | 26.8 | CAU | 6 [0.8] | |
| Trp | UGG | 15.2 | 14.3 | CCA | 1 [0.3] | |
a
The total number of codons is 1,363,498 for E. coli (4,290 protein-coding genes) and 54,574 for T4 (274 genes). Optimal codons of E. coli are underlined.
b
The cellular tRNA contents relative to Leu-tRNA with anticodon CAG are shown in brackets. Low-abundance tRNAs that are difficult to quantify by the two-dimensional gel analysis are shown as [minor].