Recombinant production of bacterial toxins and their derivatives in the methylotrophic yeast Pichia pastoris

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	1^st preference	2^nd preference	Amino acid	1^st preference	2^nd 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].