Preferences of synonymous codons and translational control during the chloroplast genome evolution

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In chloroplasts, the translation efficiencies of synonymous codons are not always correlated with their codon usage. Tobacco chloroplast rps2 mRNA contains many codons having efficient translation activity, whereas rps16 mRNA has a lot of inefficient codons. To elucidate whether the codon preference affect the translation efficiencies of these mRNAs, I analyzed the translation efficiencies of rps2 and rps16 mRNAs using the in vitro translation system from tobacco chloroplasts. I found that (1) 5'UTR of rps16 mRNA has less translation activity, (2) protein coding region of rps16 mRNA was translated about 3-times faster than that of rps2 mRNA, and (3) codon substitutions increased that translation efficiency of protein coding region of rps16 mRNA.