title: Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli.
abstract: Four independent nonsense mutations were engineered into the Escherichia coli chromosomal lacZ gene, and reversion rates back to LacZ(+) phenotypes were determined. The mutation potential of bases within putative DNA secondary structures formed during transcription was predicted by a sliding-window analysis that simulates successive folding of the ssDNA creating these structures. The relative base mutabilities predicted by the mfg computer program correlated with experimentally determined reversion rates in three of the four mutants analysed. The nucleotide changes in revertants at one nonsense codon site consisted of a triple mutation, presumed to occur by a templated repair mechanism. Additionally, the effect of supercoiling on mutation was investigated and, in general, reversion rates increased with higher levels of negative supercoiling. Evidence indicates that predicted secondary structures are in fact formed in vivo and that directed mutation in response to starvation stress is dependent upon the exposure of particular bases, the stability of the structures in which these bases are unpaired and the level of DNA supercoiling within the cell.
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Burkala
authors.affiliation: EndoBiologics Inc., Missoula, MT 59808, USA.
authors.forename: Jacqueline M
authors.initials: JM
authors.lastname: Reimers
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
authors.forename: Karen H
authors.initials: KH
authors.lastname: Schmidt
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
authors.forename: Nick
authors.initials: N
authors.lastname: Davis
authors.affiliation: University of Massachusetts, Worcester, MA 01605, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Wei
authors.affiliation: Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
authors.forename: Barbara E
authors.initials: BE
authors.lastname: Wright
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004252:DNA Mutational Analysis; D004269:DNA, Bacterial; D004278:DNA, Superhelical / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry*; D007763:Lac Operon / Q000235:genetics*; D009154:Mutation; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004278:DNA, Superhelical; D029968:Escherichia coli Proteins