title: A mathematical model for timing the release from sequestration and the resultant Brownian migration of SeqA clusters in E. coli.
abstract: DNA replication in Escherichia coli is initiated by DnaA binding to oriC, the replication origin. During the process of assembly of the replication factory, the DnaA is released back into the cytoplasm, where it is competent to reinitiate replication. Premature reinitiation is prevented by binding SeqA to newly formed GATC sites near the replication origin. Resolution of the resulting SeqA cluster is one aspect of timing for reinitiation. A Markov model accounting for the competition between SeqA binding and methylation for one or several GATC sites relates the timing to reaction rates, and consequently to the concentrations of SeqA and methylase. A model is proposed for segregation, the motion of the two daughter DNAs into opposite poles of the cell before septation. This model assumes that the binding of SeqA and its subsequent clustering results in loops from both daughter nucleoids attached to the SeqA cluster at the GATC sites. As desequestration occurs, the cluster is divided in two, one associated with each daughter. As the loops of DNA uncoil, the two subclusters migrate apart due to the Brownian ratchet effect of the DNA loop.
authors.affiliation: Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, USA. drewd@rpi.edu
authors.forename: Donald A
authors.initials: DA
authors.lastname: Drew
authors.forename: Gretchen A
authors.initials: GA
authors.lastname: Koch
authors.forename: Shannon
authors.initials: S
authors.lastname: Hitchcock
authors.forename: Jill
authors.initials: J
authors.lastname: Kowalski
authors.forename: Ronak
authors.initials: R
authors.lastname: Talati
authors.forename: Vera
authors.initials: V
authors.lastname: Valakh
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000502:physiology*; D002455:Cell Division / Q000502:physiology; D004261:DNA Replication / Q000502:physiology*; D004268:DNA-Binding Proteins / Q000502:physiology*; D004926:Escherichia coli / Q000166:cytology / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000502:physiology*; D008390:Markov Chains; D008954:Models, Biological; D018741:Replication Origin / Q000502:physiology*; D013269:Stochastic Processes
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C089746:SeqA protein, E coli