title: Anatomy of a preferred target site for the bacterial insertion sequence IS903.
abstract: Like many transposons the bacterial insertion sequence IS903 was thought to insert randomly. However, using both genetic and statistical approaches, we have derived a target site for IS903 that is used 84% of the time. Computational and genetic analyses of multiple IS903 insertion sites predicted a preferred target consisting of a 21 bp palindromic pattern centered on the 9 bp target duplication generated during transposition. Here we show that targeting can be dissected into four components: the 5 bp flanking sequences, the most important sequences required for site-specific insertion; the 7 bp palindromic core within the target duplication; the dinucleotide pair at the transposon-target junction; and the local DNA context. Finally, using a substrate with multiple target sites we show that a target site is more likely found by a local bind-and-slide model and not by extended DNA tracking.
authors.affiliation: Division of Infectious Disease, Wadsworth Center, New York State Dept. of Health, Albany, NY 12201, USA.
authors.forename: W Y
authors.initials: WY
authors.lastname: Hu
authors.forename: W
authors.initials: W
authors.lastname: Thompson
authors.forename: C E
authors.initials: CE
authors.lastname: Lawrence
authors.forename: K M
authors.initials: KM
authors.lastname: Derbyshire
mesh_terms: D000225:Adenine / Q000378:metabolism; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics / Q000502:physiology*; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D020440:Gene Duplication; D008957:Models, Genetic; D016254:Mutagenesis, Insertional / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment; D013379:Substrate Specificity; D013696:Temperature
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D000225:Adenine