Codon usage

Efficient translation depends on matching the preferred pattern of host codon usage in the heterologous gene. 

Analysis of the codon usage of the Clpgl sequence showed that 44 out of the 61 sense codons are used. Codons ending in C are preferred and represent 74.4 % of the codons used. 

In general, VFPs are preferred with optimized codon usage and containing folding mutations to facilitate expression and optimize maturation. 

Yang, T. T., Cheng, L. and Kain, S. R. (1996). Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Res. 24, 4592-3. 

Several molecular strategies have been successful in increasing foreign protein production in cultured plant cells. These include using promoters for inducible expression [10, 12, 29], optimizing codon usage [30] and adding the KDEL sequence to ensure protein retention in the endoplasmic reticulum [31]. Application of different... 

We now have clear evidence that selenium can be introduced specifically into proteins as selenocysteine and into a subset of tRNA species as mnm Se U or Se2U. The pathways and molecular mechanisms for insertion of selenium into these molecules have been well established in several model systems, the best studied being E. coli. The role for selenium in selenoproteins (i.e., the need for selenium over sulfur) is thought to be its ability to act as a more reactive nucleophile and perhaps a more rapid catalyst. However, a void in our knowledge exists for the specific need for selenium-modified tRNAs. Mutation of either selD or ybbB did not alter the growth characteristics of E. coli- however, no thorough analysis of the bacterial stress response has been carried out in any of these mutants. Clearly, further study is needed to better define the role for selenium in wobble codon usage for a subset of tRNA species. 

G. D Onolno, D. Mouchiroud, B. Aiissani, C. Gautier, and G. Bernardi, Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol. 32, 504—510 (1991). 

L. Duret, Evolution of synonymous codon usage in metazoans. Curr. Opirt Genet Dev. 12, 640-649 (2002). 

E. coli Economical, fast, easy, high yield, well characterized genetics, large number of cloning vectors Insolubility and misfolding of proteins, no glycosylation possible, difference in codon usage between prokaryotes and eukaryotes... 

Wada, K., Wada, Y., Ishibashi, E, Gojobori, T., and Ikemura, T. (1992). Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res. 20 2111-2118. 

West, S. E. H Iglewski, B. H. (1988). Codon usage in Pseudomonas aeruginosa. Nucleic Acids Research, 16, 9323-35. 

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