title: Intrastrand triplex DNA repeats in bacteria: a source of genomic instability.
abstract: Repetitive nucleic acid sequences are often prone to form secondary structures distinct from B-DNA. Prominent examples of such structures are DNA triplexes. We observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. A systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the ITxF database available online at http://bioinformatics.uni-konstanz.de/utils/ITxF/. Next we investigated biophysical and biochemical properties of a particular G/C-rich triplex motif (TM) that occurs in many copies in more than 260 bacterial genomes by CD and nuclear magnetic resonance spectroscopy as well as in vivo footprinting techniques. A characterization of putative properties and functions of these unusually frequent nucleic acid motifs demonstrated that the occurrence of the TM is associated with a high degree of genomic instability. TM-containing genomic loci are significantly more rearranged among closely related Escherichia coli strains compared to control sites. In addition, we found very high frequencies of TM motifs in certain Enterobacteria and Cyanobacteria that were previously described as genetically highly diverse. In conclusion we link intrastrand triplex motifs with the induction of genomic instability. We speculate that the observed instability might be an adaptive feature of these genomes that creates variation for natural selection to act upon.
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Isabelle T
authors.initials: IT
authors.lastname: Holder
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wagner
authors.affiliation: Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Peiwen
authors.initials: P
authors.lastname: Xiong
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Malte
authors.initials: M
authors.lastname: Sinn
authors.affiliation: Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Tancred
authors.initials: T
authors.lastname: Frickey
authors.affiliation: Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Meyer
authors.affiliation: Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany joerg.hartig@uni-konstanz.de.
authors.forename: Jörg S
authors.initials: JS
authors.lastname: Hartig
mesh_terms: D020856:AT Rich Sequence; D004247:DNA / Q000737:chemistry*; D004269:DNA, Bacterial / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D004926:Escherichia coli / Q000235:genetics; D020862:GC Rich Sequence; D016680:Genome, Bacterial; D042822:Genomic Instability; D059372:Nucleotide Motifs; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004269:DNA, Bacterial; C051802:triplex DNA; D004247:DNA