Skip to main content
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1987 Jan;84(1):166–169. doi: 10.1073/pnas.84.1.166

The guanine and cytosine content of genomic DNA and bacterial evolution.

A Muto, S Osawa
PMCID: PMC304163  PMID: 3467347

Abstract

The genomic guanine and cytosine (G + C) content of eubacteria is related to their phylogeny. The G + C content of various parts of the genome (protein genes, stable RNA genes, and spacers) reveals a positive linear correlation with the G + C content of their genomic DNA. However, the plotted correlation slopes differ among various parts of the genome or among the first, second, and third positions of the codons depending on their functional importance. Facts suggest that biased mutation pressure, called A X T/G X C pressure, has affected whole DNA during evolution so as to determine the genomic G + C content in a given bacterium. The role of A X T/G X C pressure in diversification of bacterial DNA sequences and codon usage patterns is discussed in the perspective of the neutral theory of molecular evolution.

Full text

PDF
166

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. BARBU E., LEE K. Y., WAHL R. Contenu en bases puriques et pyrimidiques des acides désoxyribonucléiques des bactéries. Ann Inst Pasteur (Paris) 1956 Aug;91(2):212–224. [PubMed] [Google Scholar]
  2. Bibb M. J., Bibb M. J., Ward J. M., Cohen S. N. Nucleotide sequences encoding and promoting expression of three antibiotic resistance genes indigenous to Streptomyces. Mol Gen Genet. 1985;199(1):26–36. doi: 10.1007/BF00327505. [DOI] [PubMed] [Google Scholar]
  3. Bird A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980 Apr 11;8(7):1499–1504. doi: 10.1093/nar/8.7.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown N. L., Ford S. J., Pridmore R. D., Fritzinger D. C. Nucleotide sequence of a gene from the Pseudomonas transposon Tn501 encoding mercuric reductase. Biochemistry. 1983 Aug 16;22(17):4089–4095. doi: 10.1021/bi00286a015. [DOI] [PubMed] [Google Scholar]
  5. Caron F., Meyer E. Does Paramecium primaurelia use a different genetic code in its macronucleus? Nature. 1985 Mar 14;314(6007):185–188. doi: 10.1038/314185a0. [DOI] [PubMed] [Google Scholar]
  6. Cerretti D. P., Dean D., Davis G. R., Bedwell D. M., Nomura M. The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene. Nucleic Acids Res. 1983 May 11;11(9):2599–2616. doi: 10.1093/nar/11.9.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cox E. C., Yanofsky C. Altered base ratios in the DNA of an Escherichia coli mutator strain. Proc Natl Acad Sci U S A. 1967 Nov;58(5):1895–1902. doi: 10.1073/pnas.58.5.1895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Helftenbein E. Nucleotide sequence of a macronuclear DNA molecule coding for alpha-tubulin from the ciliate Stylonychia lemnae. Special codon usage: TAA is not a translation termination codon. Nucleic Acids Res. 1985 Jan 25;13(2):415–433. doi: 10.1093/nar/13.2.415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hori H., Osawa S. Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species. Biosystems. 1986;19(3):163–172. doi: 10.1016/0303-2647(86)90037-7. [DOI] [PubMed] [Google Scholar]
  10. Horowitz S., Gorovsky M. A. An unusual genetic code in nuclear genes of Tetrahymena. Proc Natl Acad Sci U S A. 1985 Apr;82(8):2452–2455. doi: 10.1073/pnas.82.8.2452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 1981 Sep 25;151(3):389–409. doi: 10.1016/0022-2836(81)90003-6. [DOI] [PubMed] [Google Scholar]
  12. Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol. 1982 Jul 15;158(4):573–597. doi: 10.1016/0022-2836(82)90250-9. [DOI] [PubMed] [Google Scholar]
  13. Iwami M., Muto A., Yamao F., Osawa S. Nucleotide sequence of the rrnB 16S ribosomal RNA gene from Mycoplasma capricolum. Mol Gen Genet. 1984;196(2):317–322. doi: 10.1007/BF00328065. [DOI] [PubMed] [Google Scholar]
  14. Jukes T. H. A change in the genetic code in Mycoplasma capricolum. J Mol Evol. 1985;22(4):361–362. doi: 10.1007/BF02115692. [DOI] [PubMed] [Google Scholar]
  15. Kagawa Y., Nojima H., Nukiwa N., Ishizuka M., Nakajima T., Yasuhara T., Tanaka T., Oshima T. High guanine plus cytosine content in the third letter of codons of an extreme thermophile. DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. J Biol Chem. 1984 Mar 10;259(5):2956–2960. [PubMed] [Google Scholar]
  16. Kimura M. Evolutionary rate at the molecular level. Nature. 1968 Feb 17;217(5129):624–626. doi: 10.1038/217624a0. [DOI] [PubMed] [Google Scholar]
  17. Kimura M., Ohta T. On some principles governing molecular evolution. Proc Natl Acad Sci U S A. 1974 Jul;71(7):2848–2852. doi: 10.1073/pnas.71.7.2848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. King J. L., Jukes T. H. Non-Darwinian evolution. Science. 1969 May 16;164(3881):788–798. doi: 10.1126/science.164.3881.788. [DOI] [PubMed] [Google Scholar]
  19. Konigsberg W., Godson G. N. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Feb;80(3):687–691. doi: 10.1073/pnas.80.3.687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kuchino Y., Hanyu N., Tashiro F., Nishimura S. Tetrahymena thermophila glutamine tRNA and its gene that corresponds to UAA termination codon. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4758–4762. doi: 10.1073/pnas.82.14.4758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. MIURA K. I. The nucleotide composition of ribonucleic acids of soluble and particle fractions in several species of bacteria. Biochim Biophys Acta. 1962 Jan 22;55:62–70. doi: 10.1016/0006-3002(62)90931-9. [DOI] [PubMed] [Google Scholar]
  22. Maniloff J., Morowitz H. J. Cell biology of the mycoplasmas. Bacteriol Rev. 1972 Sep;36(3):263–290. doi: 10.1128/br.36.3.263-290.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Muto A., Kawauchi Y., Yamao F., Osawa S. Preferential use of A- and U-rich codons for Mycoplasma capricolum ribosomal proteins S8 and L6. Nucleic Acids Res. 1984 Nov 12;12(21):8209–8217. doi: 10.1093/nar/12.21.8209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Neugebauer K., Sprengel R., Schaller H. Penicillinase from Bacillus licheniformis: nucleotide sequence of the gene and implications for the biosynthesis of a secretory protein in a Gram-positive bacterium. Nucleic Acids Res. 1981 Jun 11;9(11):2577–2588. doi: 10.1093/nar/9.11.2577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ogasawara N. Markedly unbiased codon usage in Bacillus subtilis. Gene. 1985;40(1):145–150. doi: 10.1016/0378-1119(85)90035-6. [DOI] [PubMed] [Google Scholar]
  26. Preer J. R., Jr, Preer L. B., Rudman B. M., Barnett A. J. Deviation from the universal code shown by the gene for surface protein 51A in Paramecium. Nature. 1985 Mar 14;314(6007):188–190. doi: 10.1038/314188a0. [DOI] [PubMed] [Google Scholar]
  27. SUEOKA N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci U S A. 1962 Apr 15;48:582–592. doi: 10.1073/pnas.48.4.582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sawada M., Muto A., Iwami M., Yamao F., Osawa S. Organization of ribosomal RNA genes in Mycoplasma capricolum. Mol Gen Genet. 1984;196(2):311–316. doi: 10.1007/BF00328064. [DOI] [PubMed] [Google Scholar]
  29. Scott K. F., Rolfe B. G., Shine J. Nitrogenase structural genes are unlinked in the nonlegume symbiont Parasponia rhizobium. DNA. 1983;2(2):141–148. doi: 10.1089/dna.1983.2.141. [DOI] [PubMed] [Google Scholar]
  30. Shinozaki K., Yamada C., Takahata N., Sugiura M. Molecular cloning and sequence analysis of the cyanobacterial gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Proc Natl Acad Sci U S A. 1983 Jul;80(13):4050–4054. doi: 10.1073/pnas.80.13.4050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sloma A., Gross M. Molecular cloning and nucleotide sequence of the type I beta-lactamase gene from Bacillus cereus. Nucleic Acids Res. 1983 Jul 25;11(14):4997–5004. doi: 10.1093/nar/11.14.4997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Speyer J. F. Mutagenic DNA polymerase. Biochem Biophys Res Commun. 1965 Oct 8;21(1):6–8. doi: 10.1016/0006-291x(65)90417-1. [DOI] [PubMed] [Google Scholar]
  33. Thompson C. J., Gray G. S. Nucleotide sequence of a streptomycete aminoglycoside phosphotransferase gene and its relationship to phosphotransferases encoded by resistance plasmids. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5190–5194. doi: 10.1073/pnas.80.17.5190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Yamao F., Muto A., Kawauchi Y., Iwami M., Iwagami S., Azumi Y., Osawa S. UGA is read as tryptophan in Mycoplasma capricolum. Proc Natl Acad Sci U S A. 1985 Apr;82(8):2306–2309. doi: 10.1073/pnas.82.8.2306. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES