2013/01/18 by Maximilian Bauer, Max Bauer, Ralf Metzler · 2 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · Physics and Astronomy · #Bacterial Genetics and Biotechnology #Bacteriophages and microbial interactions #Diffusion and Search Dynamics #cond-mat.stat-mech #physics.bio-ph #q-bio.SC
paper · pdf · doi:10.1371/journal.pone.0053956
published as PLoS One 8, e53956 (2013) · 19 pages, 9 figures, Supplementary Information directly included
openalex publication_date 2013/01/18 · arxiv created 2013/01/23 · arxiv updated 2015/06/12 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.