title: Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection.
abstract: Nucleic acids have the potential to form intrastrand stem-loops if complementary bases are suitably located. Computer analyses of poliovirus and retroviral RNAs have revealed a reciprocal relationship between "statistically significant" stem-loop potential and "sequence variability." The statistically significant stem-loop potential of a nucleic acid segment has been defined as a function of the difference between the folding energy of the natural segment (FONS) and the mean folding energy of a set of randomized (shuffled) versions of the natural segment (FORS-M). Since FONS is dependent on both base composition and base order, whereas FORS-M is solely dependent on base composition (a genomic characteristic), it follows that statistically significant stem-loop potential (FORS-D) is a function of base order (a local characteristic). In retroviral genomes, as in all DNA genomes studied, positive FORS-D values are widely distributed. Thus there have been pressures on base order both to encode specific functions and to encode stem-loops. As in the case of DNA genomes under positive Darwinian selection pressure, in HIV-1 specific function appears to dominate in rapidly evolving regions. Here high sequence variability, expressed as substitution density (not indel density), is associated with negative FORS-D values (impaired base-order-dependent stem-loop potential). This suggests that in these regions HIV-1 genomes are under positive selection pressure by host defenses. The general function of stem-loops is recombination. This is a vital process if, from among members of viral "quasispecies," functional genomes are to be salvaged. Thus, for rapidly evolving RNA genomes, it is as important to conserve base-order-dependent stem-loop potential as to conserve other functions.
authors.affiliation: Department of Biochemistry, Queen's University, Kingston, Ontario, Canada.
authors.forename: D R
authors.initials: DR
authors.lastname: Forsdyke
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D017955:Poliovirus / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D012190:Retroviridae / Q000235:genetics*
chemical_list: D012367:RNA, Viral