ArticleProceedings of the National Academy of Sciences of the United States of America2009
DNA looping provides stability and robustness to the bacteriophage lambda switch.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- The Dynamics of Inducible Genetic Circuits.ArXiv · 2026Article
- Two novel polyvalent phages: a promising approach for cross-order pathogen control in aquaculture.Virology journal · 2025Article
- Characterization of a Vibriophage Infecting PathogenicInternational journal of molecular sciences · 2023Article
- A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.Acta crystallographica. Section D, Structural biology · 2023Article
- A Novel Vibriophage vB_VcaS_HC Containing Lysogeny-Related Gene Has Strong Lytic Ability against Pathogenic Bacteria.Virologica Sinica · 2021Article
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
- Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.ACS omega · 2020Article
- Bacterial growth: a statistical physicist's guide.Reports on progress in physics. Physical Society (Great Britain) · 2019Review
- Molecular Mechanisms Governing "Hair-Trigger" Induction of Shiga Toxin-Encoding Prophages.Viruses · 2018Article
- Path-sampling strategies for simulating rare events in biomolecular systems.Current opinion in structural biology · 2017Review
- Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.PLoS computational biology · 2016Article
- Genetic dissection of independent and cooperative transcriptional activation by the LysR-type activator ThnR at close divergent promoters.Scientific reports · 2016Article
- Pulse Detecting Genetic Circuit - A New Design Approach.PloS one · 2016Article
- Biological Sources of Intrinsic and Extrinsic Noise in cI Expression of Lysogenic Phage Lambda.Scientific reports · 2015Article
- Programmable bacteria detect and record an environmental signal in the mammalian gut.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- Quantitative influence of macromolecular crowding on gene regulation kinetics.Nucleic acids research · 2014Article
- DNA looping in prokaryotes: experimental and theoretical approaches.Journal of bacteriology · 2013Review
- Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.PLoS biology · 2013Article
- Effects of macromolecular crowding on genetic networks.Biophysical journal · 2011Article
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3 authors.
Funding
Abstract
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. We have constructed a stochastic model for this switch. Using Forward Flux Sampling simulations, we show that this model predicts an extremely low rate of spontaneous prophage induction in a recA mutant, in agreement with experimental observations. In our model, the DNA loop formed by octamerization of CI bound to the O(L) and O(R) operator regions is crucial for stability, allowing the lysogenic state to remain stable even when a large fraction of the total CI is depleted by nonspecific binding to genomic DNA. DNA looping also ensures that the switch is robust to mutations in the order of the O(R) binding sites. Our results suggest that DNA looping can provide a mechanism to maintain a stable lysogenic state in the face of a range of challenges including noisy gene expression, nonspecific DNA binding, and operator site mutations.
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