TABLE 3.
Preferred codons in six species of Saccharomyes
| Amino acid | S. bayanus | S. castelli | S. kluyveri | S. mikatae | S. paradoxus | S. cerevisiae |
|---|---|---|---|---|---|---|
| Ile | ATC 0.66 | ATT 0.51 | ATC 0.70 | ATC 0.54 | ATC 0.56 | ATC 0.58 |
| Asn | AAC 0.96 | AAC 1.00 | AAC 1.00 | AAC 0.92 | AAC 0.93 | AAC 0.94 |
| Asp | GAC 0.65 | GAT 0.50 | GAC 0.70 | GAC 0.63 | GAC 0.66 | GAC 0.65 |
| Gln | CAA 0.99 | CAA 0.98 | CAA 1.00 | CAA 0.98 | CAA 0.99 | CAA 1.00 |
| Ala | GCT 0.68 | GCT 0.69 | GCT 0.73 | GCT 0.74 | GCT 0.78 | GCT 0.80 |
| His | CAC 0.82 | CAC 0.71 | CAC 1.00 | CAC 0.84 | CAC 0.88 | CAC 0.90 |
| Thr | ACT 0.52 | ACC 0.50 | ACC 0.60 | ACT 0.51 | ACC 0.52 | ACT 0.50 |
| Tyr | TAC 0.91 | TAC 0.90 | TAC 1.00 | TAC 0.85 | TAC 0.91 | TAC 0.92 |
| Glu | GAA 0.97 | GAA 0.99 | GAA 0.94 | GAA 0.95 | GAA 0.98 | GAA 0.98 |
| Pro | CCA 0.91 | CCA 0.92 | CCA 0.96 | CCA 0.90 | CCA 0.92 | CCA 0.94 |
| Leu | TTG 0.83 | TTG 0.74 | TTG 0.95 | TTG 0.80 | TTG 0.83 | TTG 0.89 |
| Phe | TTC 0.84 | TTC 0.85 | TTC 0.86 | TTC 0.84 | TTC 0.83 | TTC 0.81 |
| Gly | GGT 0.94 | GGT 0.96 | GGT 0.95 | GGT 0.96 | GGT 0.96 | GGT 0.96 |
| Lys | AAG 0.88 | AAG 0.89 | AAG 1.00 | AAG 0.84 | AAG 0.84 | AAG 0.85 |
| Trm | TAA 0.90 | TAA 1.00 | TAA 1.00 | TAA 0.62 | TAA 0.80 | TAA 0.90 |
| Arg | AGA 0.84 | AGA 0.89 | AGA 0.93 | AGA 0.88 | AGA 0.84 | AGA 0.85 |
| Cys | TGT 0.86 | TGT 0.83 | TGT 1.00 | TGT 1.00 | TGT 1.00 | TGT 1.00 |
| Val | GTC 0.51 | GTT 0.50 | GTT 0.52 | GTT 0.60 | GTT 0.55 | GTT 0.55 |
| Ser | TCC 0.51 | TCT 0.58 | TCT 0.56 | TCT 0.53 | TCT 0.52 | TCT 0.50 |
Ten highly expressed genes of S. cerevisae (RPL11A, ENO1, TDH1, RPL4A, RPL8A, RPL9A, RPL15A, RPS2, RPS3, and RPS5) were selected, and their full-length closest homologs were identified in the other yeasts whenever possible. For each amino acid, the preferred codon and its frequency is listed for each yeast over the 10 selected proteins. Amino acids with only one codon (Met, Trp) are omitted. For most amino acids, all yeasts had the same preferred codon. For Ile, Asp, Thr, Val, and Ser, there were minor differences (indicated by italics). All of these minor differences occur when there are two commonly used codons, each with a frequency of close to 50%. For instance, in S. castelli, the preferred codon for Ile is ATT (frequency of 0.50), but the second-most preferred codon is ATC (frequency of 0.48). Similarly, in S. castelli, the preferred codon for Asp is GAT (frequency 0.50), but the second-most preferred codon is GAC (frequency 0.50). In the case of Thr, only two codons are substantially used, ACT and ACC, and these have nearly an equal frequency in each yeast. Similarly, for Ser, only TCC and TCT are substantially used, each at ∼0.5 in each yeast.