Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Nov 1;24(21):4249–4255. doi: 10.1093/nar/24.21.4249

A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand.

K Ikehara 1, F Amada 1, S Yoshida 1, Y Mikata 1, A Tanaka 1
PMCID: PMC146247  PMID: 8932380

Abstract

Base compositions were examined at every position in codons of more than 50 genes from taxonomically different bacteria and of the corresponding antisense sequences on the bacterial genes. We propose that the nonstop frame on antisense strand [NSF(a)] of GC-rich bacterial genes is the most promising sequence for newly-born genes. Reasons are: (i) NSF(a) frequently appears on the antisense strand of GC-rich bacterial genes; (ii) base compositions at three positions in the codon are nearly symmetrical between the gene having around 55% GC content and the corresponding NSF(a); (iii) amino acid compositions of actual proteins are also similar to those of hypothetical proteins from the GC-rich NSF(a); and (iv) proteins from NSF(a) of 60% or more GC content are flexible enough to adapt to various molecules encountered as novel substrates, due to the high glycine content. To support our proposition, using a computer we generated hypothetical antisense sequences with the same base compositions as of NSF(a) at each base position in the codon, and examined properties of resulting proteins encoded by the imaginary genes. It was confirmed that NSF(a) of GC-rich gene carrying about 60% GC content is competent enough for a newly-born gene.

Full Text

The Full Text of this article is available as a PDF (140.0 KB).

Selected References

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

  1. Air G. M., Coulson A. R., Fiddes J. C., Friedmann T., Hutchison C. A., 3rd, Sanger F., Slocombe P. M., Smith A. J. Nucleotide sequence of the F protein coding region of bacteriophage phiX174 and the amino acid sequence of its product. J Mol Biol. 1978 Oct 25;125(2):247–254. doi: 10.1016/0022-2836(78)90347-9. [DOI] [PubMed] [Google Scholar]
  2. Beck E., Sommer R., Auerswald E. A., Kurz C., Zink B., Osterburg G., Schaller H., Sugimoto K., Sugisaki H., Okamoto T. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 1978 Dec;5(12):4495–4503. doi: 10.1093/nar/5.12.4495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Fiers W., Contreras R., Haegemann G., Rogiers R., Van de Voorde A., Van Heuverswyn H., Van Herreweghe J., Volckaert G., Ysebaert M. Complete nucleotide sequence of SV40 DNA. Nature. 1978 May 11;273(5658):113–120. doi: 10.1038/273113a0. [DOI] [PubMed] [Google Scholar]
  4. Ikehara K., Okazawa E. Unusually biased nucleotide sequences on sense strands of Flavobacterium sp. genes produce nonstop frames on the corresponding antisense strands. Nucleic Acids Res. 1993 May 11;21(9):2193–2199. doi: 10.1093/nar/21.9.2193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kanagawa K., Negoro S., Takada N., Okada H. Plasmid dependence of Pseudomonas sp. strain NK87 enzymes that degrade 6-aminohexanoate-cyclic dimer. J Bacteriol. 1989 Jun;171(6):3181–3186. doi: 10.1128/jb.171.6.3181-3186.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Keese P. K., Gibbs A. Origins of genes: "big bang" or continuous creation? Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9489–9493. doi: 10.1073/pnas.89.20.9489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Muto A., Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci U S A. 1987 Jan;84(1):166–169. doi: 10.1073/pnas.84.1.166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Negoro S., Kakudo S., Urabe I., Okada H. A new nylon oligomer degradation gene (nylC) on plasmid pOAD2 from a Flavobacterium sp. J Bacteriol. 1992 Dec;174(24):7948–7953. doi: 10.1128/jb.174.24.7948-7953.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Okada H., Negoro S., Kimura H., Nakamura S. Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature. 1983 Nov 10;306(5939):203–206. doi: 10.1038/306203a0. [DOI] [PubMed] [Google Scholar]
  10. Osawa S., Jukes T. H., Muto A., Yamao F., Ohama T., Andachi Y. Role of directional mutation pressure in the evolution of the eubacterial genetic code. Cold Spring Harb Symp Quant Biol. 1987;52:777–789. doi: 10.1101/sqb.1987.052.01.087. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Sanger F., Coulson A. R., Friedmann T., Air G. M., Barrell B. G., Brown N. L., Fiddes J. C., Hutchison C. A., 3rd, Slocombe P. M., Smith M. The nucleotide sequence of bacteriophage phiX174. J Mol Biol. 1978 Oct 25;125(2):225–246. doi: 10.1016/0022-2836(78)90346-7. [DOI] [PubMed] [Google Scholar]
  13. Shaw D. C., Walker J. E., Northrop F. D., Barrell B. G., Godson G. N., Fiddes J. C. Gene K, a new overlapping gene in bacteriophage G4. Nature. 1978 Apr 6;272(5653):510–515. doi: 10.1038/272510a0. [DOI] [PubMed] [Google Scholar]
  14. Tsuchiya K., Fukuyama S., Kanzaki N., Kanagawa K., Negoro S., Okada H. High homology between 6-aminohexanoate-cyclic-dimer hydrolases of Flavobacterium and Pseudomonas strains. J Bacteriol. 1989 Jun;171(6):3187–3191. doi: 10.1128/jb.171.6.3187-3191.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Yomo T., Urabe I., Okada H. No stop codons in the antisense strands of the genes for nylon oligomer degradation. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3780–3784. doi: 10.1073/pnas.89.9.3780. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES