title: A novel mutational hotspot in a natural quasipalindrome in Escherichia coli.
abstract: We have found that most spontaneous mutations in the thyA gene of Escherichia coli selected for resistance to trimethoprim result from a TA to AT transversion at a single site within an imperfect inverted repeat or quasipalindrome sequence. This natural quasipalindrome within the coding region of thyA contains an extraordinarily potent hotspot for mutation. Our analysis provides evidence that these mutations are templated by nearby sequences by replication within a hairpin structure. Although quasipalindrome-associated mutations have been observed in many organisms, including humans, the cellular avoidance mechanisms for these unusual mutational events have remained unexplored. We find that the mutational hotspot in thyA is dramatically stimulated by inactivation of exonucleases I and VII, which degrade single-strand DNA with a common 3'-5' polarity. We propose that these exonucleases abort the replicative misalignment events that initiate hairpin-templated mutagenesis by degrading displaced nascent DNA strands. Mismatch repair-defective strains also showed increased mutability at the hotspot, consistent with the notion that these mutations arise during chromosomal lagging-strand replication and are often subsequently removed by methyl-directed mismatch repair. The absence of the thyA quasipalindrome sequence from other related bacterial genera suggests that this sequence represents a "selfish" DNA element whose existence itself is driven by this unusual hairpin-templating mechanism.
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA, 02454-9110, USA.
authors.forename: M
authors.initials: M
authors.lastname: Viswanathan
authors.forename: J J
authors.initials: JJ
authors.lastname: Lacirignola
authors.forename: R L
authors.initials: RL
authors.lastname: Hurley
authors.forename: S T
authors.initials: ST
authors.lastname: Lovett
mesh_terms: D000892:Anti-Infective Agents, Urinary / Q000494:pharmacology; D020137:Base Pair Mismatch / Q000235:genetics; D001483:Base Sequence; D004252:DNA Mutational Analysis; D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics*; D004269:DNA, Bacterial / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D005090:Exodeoxyribonucleases / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial / Q000235:genetics; D007700:Kinetics; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics*; D009154:Mutation / Q000235:genetics*; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D013698:Templates, Genetic; D014295:Trimethoprim / Q000494:pharmacology; D014296:Trimethoprim Resistance / Q000235:genetics
chemical_list: D000892:Anti-Infective Agents, Urinary; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D014295:Trimethoprim; D005090:Exodeoxyribonucleases; C028450:exodeoxyribonuclease I; C026870:exodeoxyribonuclease VII