Table 2.
P. pastoris codon preference. This codon preference table was compiled from literature and is based on highly expressed genes in P. pastoris, as well as those in other yeast species such as S. cerevisiae [44, 51-53].
| Amino acid | 1st preference | 2nd preference | Amino acid | 1st preference | 2nd preference |
| Ala (A) | GCT | GCC | Leu (L) | TTG | CTT/CTG |
| Arg (R) | AGA | CGT | Lys (K) | AAG | AAA§ |
| Asn (N)* | AAC | AAT | Met (M) | ATG | - |
| Asp (D) | GAC | GAT | Phe (F) | TTC | TTT§ |
| Cys (C)* | TGT | TGC | Pro (P) | CCA | CCT |
| Gln (Q)† | CAA | CAG | Ser (S)† | TCT | TCC |
| Glu (E)‡ | GAG | GAA | Thr (T)† | ACT | ACC |
| Gly (G) | GGT | GGA | Trp (W) | TGG | - |
| His (H)* | CAC | CAT | Tyr (Y)* | TAC | TAT |
| Ile (I)† | ATT | ATC | Val (V) | GTT | GTC |
†Amino acids for which there is a minimal bias between the first and second-most preferred codons; ‡rare amino acids constituting a major discrepancy between the P. pastoris and S. cerevisiae codon preferences; *amino acids with a very high bias for the first preference codon. Other general trends observed with yeast codon preferences are as follows: (1) §codons that contain 100% G, C, A or T are best avoided, (2) there is a strong avoidance of side-by-side GC base pairs in codon-anticodon interactions, (3) there are three codons used for translational termination, which are used with the frequency TAA > TAG > TGA, and (4) the S. cerevisiae consensus sequence for translation initiation context is A/Y A A/U A AUG UCU (where Y is a pyrimidine base, C or T), however it has been shown to have only a moderate effect on translation [51, 53, 54].