‘Entropy-Based mechanism of ribosome-nucleoid segregation in E. coli cells’
Open accessAbstract
In Escherichia coli, ribosomes concentrate near the cylindrical wall and at the endcaps, whereas the chromosomal DNA segregates in the more centrally located nucleoid. A simple statistical model recovers the observed ribosome-nucleoid segregation remarkably well. Plectonemic DNA is represented as a hyperbranched hard-sphere polymer, and multiple ribosomes that simultaneously translate the same mRNA strand (polysomes) are represented as freely jointed chains of hard spheres. There are no attractive interactions between particles, only excluded-volume effects. At realistic DNA and ribosome concentrations, segregation arises primarily from two effects: the DNA polymer avoids walls to maximize conformational entropy, and the polysomes occupy the empty space near the walls to maximize translational entropy. In this complex system, maximizing total entropy results in spatial organization of the components. Due to coupling of mRNA to DNA through RNA polymerase, the same entropic effects should favor the placement of highly expressed genes at the interface between the nucleoid and the ribosome-rich periphery. Such a placement would enable efficient cotranscriptional translation and facile transertion of membrane proteins into the cytoplasmic membrane. Finally, in the model, monofunctional DNA polymer beads representing the tips of plectonemes preferentially locate near the cylindrical wall. This suggests that initiation of transcription may occur preferentially near the ribosome-rich periphery.
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Excluded volume interactions of ribosomes have a significant influence on nucleoid organization.
“Due to the size and near-uniform distribution of ribosomes present in the cytosol, the excluded volume interactions of these protein-RNA complexes are known to have a significant influence on the nucleoid organization (Mondal et al., 2011).”
From Molecular dynamics simulation of an entire cell (2023) · cites this paper as Mondal et al., 2011
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Molecular dynamics simulation of an entire cell
Stevens, J. A., Grünewald, F., van Tilburg, P. A. M., König, M., Gilbert, B. R., Brier, T. A., Thornburg, Z. R., Luthey-Schulten, Z., & Marrink, S. J. (2023) · Frontiers in Chemistry · doi:10.3389/fchem.2023.1106495 · Cited by 156 · see citing works
“Due to the size and near-uniform distribution of ribosomes present in the cytosol, the excluded volume interactions of these protein-RNA complexes are known to have a significant influence on the nucleoid organization (Mondal et al., 2011).”
BackgroundToward a Whole-Cell model of ribosome biogenesis: kinetic modeling of SSU assembly
Earnest, E. E., Lai, J., Chen, K., Hallock, M. J., Williamson, J. R., & Luthey-Schulten, Z. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.07.030 · Cited by 30 · see citing works
Dynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19 · see citing works
“Before we try to quantify how the effects of these coupled mechanisms affect the spatial organization and diffusion of the chromosome and ribosomes (Mondal et al., 2011), here we quantify how the chromosome and complete, intact ribosomes affect the diffusion of one another at the scale of a whole…”
- Authors
- Mondal, J., Bratton, B. P., Li, Y., Yethiraj, A., & Weisshaar, J. C.
- Affiliations
- University of Wisconsin–Madison (US)
- Corresponding author
- Yethiraj, Arun
- Weisshaar, James C.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2011-06
- Volume
- 100
- Issue
- 11
- Pages
- 2605-2613
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC3117155
- OpenAlex
- W1990823004
- Cited by
- 110
- References
- 54
- Citations by year
- 2026: 2 · 2025: 12 · 2024: 8 · 2023: 11 · 2022: 5 · 2021: 9 · 2020: 10 · 2019: 13 · 2018: 10 · 2017: 5 · 2016: 3 · 2015: 9 · 2014: 7 · 2013: 3 · 2012: 2
- FWCI
- 1.69
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (T32GM08293, R01GM086468, T32GM008293)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Escherichia coli, nucleoid, ribosome localization, excluded volume, conformational entropy, translational entropy, polysomes, transcription initiation, cell wall
- MeSH terms
- Cell Nucleus, DNA, Bacterial, Escherichia coli, Models, Molecular, Nucleic Acid Conformation, Ribosomes, Entropy
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