ArticleProceedings of the National Academy of Sciences of the United States of America2007
How gene order is influenced by the biophysics of transcription regulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 188 citations in OpenAlex.
- Early Evolution of the Prokaryotic Transcription Factor Repertoire.Genome biology and evolution · 2026Article
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- Modeling Facilitated Diffusion of Proteins in Crowded Environment.Sub-cellular biochemistry · 2025Review
- Transcription Factors behindPlants (Basel, Switzerland) · 2024Article
- A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice.Nature communications · 2024Article
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- Toward Memory in a DNA Brush: Site-Specific Recombination Responsive to Polymer Density, Orientation, and Conformation.Journal of the American Chemical Society · 2023Article
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- Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study.Microbial biotechnology · 2022Article
- Dynamics of Proteins and Macromolecular Machines in Escherichia coli.EcoSal Plus · 2021Review
- The economy of chromosomal distances in bacterial gene regulation.NPJ systems biology and applications · 2021Article
- Quasi-robust control of biochemical reaction networks via stochastic morphing.Journal of the Royal Society, Interface · 2021Article
- Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors.Molecules (Basel, Switzerland) · 2021Review
- From deterministic to fuzzy decision-making in artificial cells.Nature communications · 2020Article
- Guided nuclear exploration increases CTCF target search efficiency.Nature chemical biology · 2020Article
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- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
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- Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity.Scientific reports · 2019Article
- Chromatin Configuration Affects the Dynamics and Distribution of a Transiently Interacting Protein.Biophysical journal · 2018Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.
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