Translation efficiencies of synonymous codons for arginine differ dramatically and are not correlated with codon usage in chloroplasts

Codon usage in chloroplast mRNAs is different from that in prokaryotic and cytosolic mRNAs. We previously devised an in vitro assay for translation efficiencies using synthetic mRNAs, and measured translation efficiencies of five synonymous codon groups in tobacco chloroplasts. Using this assay, we here report our analysis of four additional synonymous codon groups in tobacco chloroplasts. We found that translation efficiencies of three arginine codons AGA, CGU and CGA differ dramatically, ca. 10-fold difference although the three arginine codons possess similar codon usage. Translation of AGA is very high, while CGA is translated extremely low. CGA is used frequently in chloroplasts but rare in Escherichia coli. The single tRNA species reads two histidine codons (CAU and CAC) and this is also the case for two glutamic acid codons (GAA and GAG) and two arginine codons (GCU and GCA). Their translation efficiencies, however, differ significantly. These observations suggest that individual codons posses their intrinsic efficiencies.