Table 1.
Investigated codon exchanges in a wild type Bacillus subtilis lipase A protein, codon usage, X/Y ratio, and classification
| Position within amino acid sequence | Investigated nucleotide triplet | Investigated codon | Codon usage in E. coli a | Recognized by tRNA | Relative tRNA content in E. coli b | Arithmetic mean X/Y ratio | Standard deviationc | Classification into Type A or Type Bd |
|---|---|---|---|---|---|---|---|---|
| Arg107 | CGT (WT) | CGU (WT) | 0.42 | Arg: 1, 2 | 0.90 | 2.0 | 0.2 (8) | A |
| Arg107 | AGA | AGA | 0.04 | Arg: AGR | Minor | 6.2 | 1.6 (3) | A |
| Arg107 | AGG | AGG | 0.03 | Arg: AGR | Minor | 8.8 | 1.1 (4) | A |
| Arg107 | CGA | CGA | 0.05 | Arg: 1, 2 | 0.90 | 13.4 | 1.1 (3) | A |
| Arg107 | CGC | CGC | 0.37 | Arg: 1, 2 | 0.90 | 0.8 | 0.2 (4) | B |
| Arg107 | CGG | CGG | 0.08 | Arg: CGG | Minor | 0.7 | 0.0 (4) | B |
| Leu143 | TTA (WT) | UUA (WT) | 0.11 | Leu: UUR | 0.25 | 2.0 | 0.2 (8) | A |
| Leu143 | CTA | CUA | 0.03 | Leu: CUA | Minor | 1.1 | 0.1 (4) | B |
| Leu143 | CTC | CUC | 0.10 | Leu: 2 | 0.30 | 1.9 | 0.2 (4) | A |
| Leu143 | CTG | CUG | 0.55 | Leu: 1 | 1.00 | 0.9 | 0.0 (3) | B |
| Leu143 | CTT | CUU | 0.10 | Leu: 2 | 0.30 | 2.4 | 0.5 (4) | A |
| Leu143 | TTG | UUG | 0.11 | Leu: UUR | 0.25 | 3.1 | 0.2 (4) | A |
E. coli BL21(DE3) clones containing plasmid pET22b(+) harboring the gene encoding His6–LOV–BSLA with wild type BSLA sequence composed of 181 amino acids. The wild type nucleotide triplets at positions 107 (arginine; Arg107) and 143 (leucine; Leu143) were changed into all possible synonymous triplets (1st and 2nd column). The investigated E. coli clones were named according to the nucleotide triplets within the gene. For all respective codons within the mRNA of E. coli (3rd column) the codon usage is given [44, 45] (4th column). For all codons the respective recognizing tRNA (5th column) and its relative contents in E. coli (6th column) are presented [39, 49]. The arithmetic mean of the X/Y ratio (Additional file 1) as well as the standard deviation according to Rahmen et al. [23] were determined for all individual cultivations of all clones (7th and 8th column). According to the critical X/Y ratio [23], all investigated clones are classified into Type A or Type B group (9th column)
aAbundance of respective codon relative to all codons for particular amino acid [44, 45]
bTaken from [39, 49]; the content is the relative amount to that of tRNALeu:1(CUG) that is normalized to 1.0 and approximately on the order of 104 molecules per cell for normally growing E. coli [49]
cIn brackets: number of individual cultivations used for calculation of arithmetic mean X/Y ratio and standard deviation
dCorresponding to critical X/Y ratio [23]