Codon usage tables

If other codon-usage tables will be used, just download the desired codon usage files from www.kazusa.or.jp/codon and add a first line containing the threshold below which codons should be regarded as pseudo stop codons. 

Figure 1. Sequence of spinach ACP-I synthetic gene. The DNA sequence was designed based on the amino acid sequence of spinach ACP I (4) and codons were chosen using a plant codon usage table.

Another peculiarity of the mitochondrial code emerged from a study of yeast codon usage. By comparing tables 29.3 and 29.1, you will see that the mitochondrial code has several differences in code word meaning. The codons beginning with CU represent Thr instead of Leu, the AUA codon represents Met instead of He, and the UGA codon represents Trp rather than a stop signal. 

Table 5.2 Comparison of D. discoideum and human codon usage... 

In order to synthesise proteins, mitochondria require ribosomes, together with a full complement of tRNAs. To use all of the codons, making allowance for wobble in the third position of the codon, it would be expected that 32 different tRNAs would be required. Mitochondrial translation apparatus has been found not only to have slightly different codon usage (see Table 8.5) but also to use a more extensive wobble ( superwobble ) than the cytoplasmic system, and this enables them to incorporate all the amino acids with only 22 tRNAs. 

In order to optimize codon usage in a synthetic gene, the frequency of codon usage must be included with the run (Fig. 3). Codon frequency is determined using the method of Nakamura et al. (8). The codon frequency table also directs the reverse translation of amino acids to codons. The format is that of the GCG Wisconsin Package. 

The GC composition of the open reading frame for pre-pro-C VF is 43.5% (for the whole cDNA 42.4%). This is approximately the same as for cobra C3 (25), though more than 10% lower than found for mammalian C3s. Similarly, the codon usage for CVF closely resembles that of cobra C3 (Table I). The significance of these differences is not known and may reflect a different preference in codon usage in the species cobra since the GC percentage of cobra nerve growth factor (43.6%) and cobra acetylcholin receptor (44.2%) are similarly low (26,27). 

In a comparison of supernatant and ribosomal tRNA populations, Wettstein [55] had found that Leu-tRNAi, which accounts for more than 50% of coli Leu-tRNA, is present much less frequently in ribosomal fractions than is the second fraction (MAK peak 2) and that, in T4-infected cells, it is largely excluded from the ribosomal fraction. In an extension of this work, Sueoka and Kano-Sueoka [56] obtained polysomal, ribosomal, and supernatant fractions from noninfected cells, as well as from infected cells, 1.5, 3, 6, and 10 minutes after T2 infection. Transfer RNA was then isolated from the various fractions, deacylated, and reacylated with radioactive leucine. The proportion of the various Leu-tRNA species in each preparation was analyzed by MAK chromatography. As shown in Table I, the Leu-tRNAi content of the polysomal fraction, which amounted to 20% of total Leu-tRNA before infection, fell to 6% within 1.5 minutes after infection and then remained essentially constant up to 10 minutes, suggesting a reduced usage of this species and consequently of the CpUpG codon. 

In addition to the frequencies that are determined by the choice of Codon Table, the user also has the opportunity to select a usage frequency Threshold. This is used as a cutoff, where any codon below the Threshold frequency is treated as if its frequency were zero, so it is never selected in backtranslation. This allows a user to exclude rare codons. 

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