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Journal of Molecular Evolution

, Volume 51, Issue 4, pp 353–362 | Cite as

Are Noncoding Sequences of Rickettsia prowazekii Remnants of ``Neutralized'' Genes?

  • Dirk  Holste
  • Olaf  Weiss
  • Ivo  Grosse
  • Hanspeter  Herzel

Abstract.

It has been hypothesized that a large fraction of 24% noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of noncoding DNA. However, a comparison with other genomes also having a low overall G+C content shows that this argument would also apply to other bacteria. To test this hypothesis, we study the coding potential in sets of genes, pseudogenes, and intergenic regions. We find that the correlation function and the χ2-measure are clearly indicative of the coding function of genes and pseudogenes. However, both coding potentials make almost no indication of a preexisting reading frame in the remaining 23% of noncoding DNA. We simulate the degradation of genes due to single-nucleotide substitutions and insertions/deletions and quantify the number of mutations required to remove indications of the reading frame. We discuss a reduced selection pressure as another possible origin of this comparatively large fraction of noncoding sequences.

Key words: Intergenic DNA — Periodicities — Reading frame — G+C content — Coding potential — Spontaneous mutation —Rickettsia prowazekii 

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Copyright information

© Springer-Verlag New York Inc. 2000

Authors and Affiliations

  • Dirk  Holste
    • 1
  • Olaf  Weiss
    • 2
  • Ivo  Grosse
    • 3
  • Hanspeter  Herzel
    • 2
  1. 1.Department of Theoretical Biophysics, Humboldt University Berlin, Invalidenstr. 42, D-10115, Berlin, GermanyDE
  2. 2.Institute for Theoretical Biology, Humboldt University Berlin, Invalidenstr. 43, D-10115, Berlin, GermanyDE
  3. 3.Institute for Molecular Biology and Biochemistry, Free University Berlin, Arnimallee 22, D-14195, Berlin, GermanyDE

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