title: Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome.
abstract: Off-rates of proteins from the DNA double helix are widely considered to be dependent only on the interactions inside the initially bound protein-DNA complex and not on the concentration of nearby molecules. However, a number of recent single-DNA experiments have shown off-rates that depend on solution protein concentration, or "facilitated dissociation." Here, we demonstrate that this effect occurs for the major Escherichia coli nucleoid protein Fis on isolated bacterial chromosomes. We isolated E. coli nucleoids and showed that dissociation of green fluorescent protein (GFP)-Fis is controlled by solution Fis concentration and exhibits an "exchange" rate constant (kexch) of ≈10(4) M(-1) s(-1), comparable to the rate observed in single-DNA experiments. We also show that this effect is strongly salt dependent. Our results establish that facilitated dissociation can be observed in vitro on chromosomes assembled in vivo
  
  
  
  Bacteria are important model systems for the study of gene regulation and chromosome dynamics, both of which fundamentally depend on the kinetics of binding and unbinding of proteins to DNA. In experiments on isolated E. coli chromosomes, this study showed that the prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration, similar to that observed in in vitro experiments. Therefore, the free cellular DNA-binding protein concentration can strongly affect lifetimes of proteins bound to the chromosome and must be taken into account in quantitative considerations of gene regulation. These results have particularly profound implications for transcription factors where DNA binding lifetimes can be a critical determinant of regulatory function.
authors.affiliation: Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA.
authors.forename: Nastaran
authors.initials: N
authors.lastname: Hadizadeh
authors.affiliation: Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.
authors.forename: Reid C
authors.initials: RC
authors.lastname: Johnson
authors.affiliation: Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA john-marko@northwestern.edu.
authors.forename: John F
authors.initials: JF
authors.lastname: Marko
mesh_terms: D002876:Chromosomes, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D035021:Factor For Inversion Stimulation Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D014157:Transcription Factors