identification of dna motifs implicated in maintenance of bacterial core genomes by predictive modeling识别的dna图案涉及维护核心细菌基因组的预测建模.pdfVIP

Identification of DNA Motifs Implicated in Maintenance of Bacterial Core Genomes by Predictive Modeling 1 ´ ` 2 2 ´ 3 2 1 David Halpern , Helene Chiapello , Sophie Schbath , Stephane Robin , Christelle Hennequet-Antier , Alexandra Gruss , 1* Meriem El Karoui ´ ´ ` ´ ´ ´ 1 INRA, UR888, Unite des Bacteries Lactiques et pathogenes Opportunistes, Jouy en Josas, France, 2 INRA, UR1077, Unite Mathematique, Informatique, et Genome, Jouy en ´ ´ ´ Josas, France, 3 AgroParisTech/INRA, UMR518, Unite Mathematiques et Informatique appliquees, Paris, France Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements. Protection of the genome likely depends on specific DNA motifs that impose limits on the regions that undergo recombination. Although most such motifs remain unidentified, they are theoretically predictable based on their genomic distribution properties. We examined the distribution of the ‘‘crossover hotspot instigator,’’ or Chi, in Escherichia coli, and found that its exceptional distribution is restricted to the core genome common to three strains. We then formulated a set of criteria that were incorporated in a statistical model to search core genomes for motifs potentially involved in genome stability in other species. Our strategy led us to identify and biologically validate two distinct heptamers that possess Chi properties, one in Staphylococcus