SELECTION ON THE CODON BIAS OF CHLAMYDOMONAS-REINHARDTII CHLOROPLAST GENES AND THE PLANT PSBA GENE

Plant chloroplast genes have a codon use that reflects the genome comp ositional bias of a high A+T content with the single exception of the highly translated psbA gene which codes for the photosystem II D1 prot ein, The codon usage of plant psbA corresponds more closely to the lim ited tRNA population of the chloroplast and is very similar to the cod on use observed in the chloroplast genes of the green alga Chlamydomon as reinhardtii. This pattern of codon use may be an adaptation for inc reased translation efficiency. A correspondence between codon use of p lant psbA and Chlamydomonas chloroplast genes and the tRNAs coded by t he chloroplast genome, however, is not observed in all synonymous codo n groups. It is shown here that the degree of correspondence between c odon use and tRNA population in different synonymous groups is correla ted with the second codon position composition. Synonymous groups with an A or T at the second codon position have a high representation of codons for which a complementary tRNA is coded by the chloroplast geno me. Those with a G or C at the second position have an increased repre sentation of codons that bind a chloroplast tRNA by wobble, It is prop osed that the difference between synonymous groups in terms of codon a daptation to the tRNA population in plant psbA and Chlamydomonas chlor oplast genes may be the result of differences in second position compo sition.