Advertisement

Journal of Molecular Evolution

, Volume 37, Issue 3, pp 273–280 | Cite as

Chloroplast DNA codon use: Evidence for selection at the psb A locus based on tRNA availability

  • Brian R. Morton
Article

Abstract

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

Key words

Codon use psb A Chloroplast genome Selection 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Aota S-I, Ikemura T (1986) Diversity in G + C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res 14:6345–6355Google Scholar
  2. Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1–11Google Scholar
  3. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953–958Google Scholar
  4. Devereux J, Haeberli H, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395PubMedGoogle Scholar
  5. D'Onofrio G, Mouchiroud D, Aissani B, Gautier C, Bernardi G (1991) Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 32:504–510Google Scholar
  6. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521–565Google Scholar
  7. Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980) Codon catalog usage and the genome hypothesis. Nucleic Acids Res 8:r49-r62Google Scholar
  8. Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9:r43-r74Google Scholar
  9. Grantham R, Perrin P, Mouchiroud D (1986) Patterns in codon usage of different kinds of species. Oxford Surveys Evol Biol 3:49–81Google Scholar
  10. Hasegawa M, Yasunaga T, Miyata T (1979) Secondary structure of MS2 phage RNA and bias in code word usage. Nucleic Acids Res 7:2073–2079Google Scholar
  11. Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun C-R, Meng B-Y, Li Y-Q, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185–194Google Scholar
  12. Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 146:1–21Google Scholar
  13. Ikemura T (1982) Correlation between the abundance of yeast tRNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 158:573–597Google Scholar
  14. Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13–35Google Scholar
  15. Mullet JE, Klein RR (1987) Transcription and RNA stability are important determinants of higher plant chloroplast RNA levels. EMBO J 6:1571–1579Google Scholar
  16. Pfitzinger H, Weil JH, Pillay DTN, Guillemaut P (1990) Codon recognition mechanisms in plant chloroplasts. Plant Mol Biol 14:805–814Google Scholar
  17. Sharp PM, Li W-H (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28–38Google Scholar
  18. Sharp PM, Li W-H (1987) The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295Google Scholar
  19. Sharp PM, Rogers MS, McConnell DJ (1985) Selection pressures on codon usage in the complete genome of bacteriophage T7. J Mol Evol 21:150–160Google Scholar
  20. Sharp PM, Tuohy TMF, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5139Google Scholar
  21. Shields DC (1990) Switches in species-specific codon preferences: the influence of mutation biases. J Mol Evol 31:71–80Google Scholar
  22. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Suguira M (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5: 2043–2049Google Scholar
  23. Umesono K, Yasuhiko S, Takeuchi M, Chang Z, Aota S-I, Inokuchi H, Ozeki H (1988) Structure and organization of Marchantia polymorpha chloroplast genome I. Cloning and gene identification. J Mol Biol 203:281–298Google Scholar
  24. Wada K-n, Aota S-i, Tsuchiya R, Ishibashi F, Gojobori T, Ikemura T (1990) Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res 18:2367–2411Google Scholar

Copyright information

© Springer-Verlag New York Inc 1993

Authors and Affiliations

  • Brian R. Morton
    • 1
  1. 1.Department of Botany and Plant SciencesUniversity of CaliforniaCARiversideUSA

Personalised recommendations