The global intrinsic curvature of archaeal and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation

Nucleic Acids Res. 2000 Jun 15;28(12):2431-8. doi: 10.1093/nar/28.12.2431.

Abstract

Until now, the genomic DNA of all eubacteria analyzed has been hyper-curved, its global intrinsic curvature being higher than that of a random sequence. In contrast, that rule failed for archaea or eukaryotes, which could be either hypo- or hyper-curved. The existence of the rule suggested that, at least for eubacteria, global intrinsic curvature is adaptive. However, the present results from analyzing 21 eubacterial and six archaeal genomes argue against adaptation. First, there are two eubacterial exceptions to the former rule. More significantly, we found that the dinucleotide composition of the genome alone (which lacks all sequence information) is enough to determine the genome curvature. Additional evidence against adaptation came from showing that the global curvature of bacterial genomes could not have evolved under either of two complementary models of curvature selection: (i) that curvature is selected locally from unbiased variability; (ii) that curvature is established globally through the selection of a curvature-altering mutational bias. We found that the observed relationship between curvature and dinucleotide composition is incompatible with model (i). We also found that, contrary to the predictions of model (ii), the dinucleo-tide compositions of bacterial genomes were not statistically special in their curvature-related properties (when compared to stochastically generated dinucleotide compositions).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • DNA, Archaeal / chemistry*
  • DNA, Bacterial / chemistry*
  • Databases, Factual
  • Dinucleoside Phosphates / chemistry
  • Genome, Archaeal*
  • Genome, Bacterial*
  • Markov Chains
  • Models, Genetic
  • Nucleic Acid Conformation*

Substances

  • DNA, Archaeal
  • DNA, Bacterial
  • Dinucleoside Phosphates