title: Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo.
abstract: The search for specific sequences on long genomes is a key process in many biological contexts. How can specific target sequences be located with high efficiency, within physiologically relevant times? We addressed this question for viral integration, a fundamental mechanism of horizontal gene transfer driving prokaryotic evolution, using the infection of Escherichia coli bacteria with bacteriophage λ and following the establishment of a lysogenic state. Following the targeting process in individual live E. coli cells in real time revealed that λ DNA remains confined near the entry point of a cell following infection. The encounter between the 15-bp-long target sequence on the chromosome and the recombination site on the viral genome is facilitated by the directed motion of bacterial DNA generated during chromosome replication, in conjunction with constrained diffusion of phage DNA. Moving the native bacterial integration site to different locations on the genome and measuring the integration frequency in these strains reveals that the frequencies of the native site and a site symmetric to it relative to the origin are similar, whereas both are significantly higher than when the integration site is moved near the terminus, consistent with the replication-driven mechanism we propose. This novel search mechanism is yet another example of the exquisite coevolution of λ with its host.
authors.affiliation: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel; and.
authors.forename: Asaf
authors.initials: A
authors.lastname: Tal
authors.affiliation: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel; and.
authors.forename: Rinat
authors.initials: R
authors.lastname: Arbel-Goren
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201.
authors.forename: Nina
authors.initials: N
authors.lastname: Costantino
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201 joel.stavans@weizmann.ac.il courtd@mail.nih.gov.
authors.forename: Donald L
authors.initials: DL
authors.lastname: Court
authors.affiliation: Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel; and joel.stavans@weizmann.ac.il courtd@mail.nih.gov.
authors.forename: Joel
authors.initials: J
authors.lastname: Stavans
mesh_terms: D010582:Bacteriophage lambda / Q000235:genetics*; D001665:Binding Sites; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000648:ultrastructure*; D004279:DNA, Viral / Q000235:genetics*; D004058:Diffusion; D004926:Escherichia coli / Q000378:metabolism / Q000821:virology*; D016679:Genome, Viral; D008164:Luminescent Proteins / Q000378:metabolism; D008242:Lysogeny; D011995:Recombination, Genetic; D014764:Viral Proteins / Q000235:genetics; D016662:Virus Integration; D000097573:Red Fluorescent Protein
chemical_list: D004279:DNA, Viral; D008164:Luminescent Proteins; D014764:Viral Proteins; D000097573:Red Fluorescent Protein
keywords: establishment of lysogeny; target location; viral transduction