Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?
Abstract
:1. Introduction
2. Coupling of Chromosomal Gene Order and Transcription
3. Gradients of Regulators
4. DNA Supercoiling Gradient and Genomic Sequence Organization
5. Role of Local Sequence Organization
6. Topological Domains
7. Modulation of the Transcriptional Supercoiling Response by NAPs
8. Coupling of DNA Structure to Function Using Two Types of DNA Information
9. Role for Changing Chromosome Configuration in Organizing Genomic Transcription
10. Coupling of DNA Topology, NAP Binding Effects, and Holoenzyme Sigma-Factor Composition: Major Regulatory Events during the E. coli Growth Cycle
11. Genomic Transcription during the Bacterial Growth Cycle Is Steered by Supercoil Energy
12. Spatially Shifting Superhelicity Optimum Determines the Temporal Gene Expression
13. The Temporal Gradient of Superhelicity Reflects the Gradient of Ion Composition and Intracellular pH
14. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Promoter | Distance from OriC (bp) | Condition | Optimal * Superhelical Density (σ) | #References |
---|---|---|---|---|
hisR | 62,500 | In vitro | ~−0.08 to −0.1 | [172] |
rrnAP1 | 120,000 | In vitro | ~−0.076 | [99] |
fis | 508,500 | In vitro & in vivo | ~−0.07-to −0.08 | [39] |
tyrT | 1,967,600 | In vitro | ~−0.05–0.06 | [83] |
osmE | 2,097,900 | In vitro | ~−0.03–0.04 | [156] |
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Muskhelishvili, G.; Sobetzko, P.; Travers, A. Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle? Biomolecules 2022, 12, 831. https://doi.org/10.3390/biom12060831
Muskhelishvili G, Sobetzko P, Travers A. Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle? Biomolecules. 2022; 12(6):831. https://doi.org/10.3390/biom12060831
Chicago/Turabian StyleMuskhelishvili, Georgi, Patrick Sobetzko, and Andrew Travers. 2022. "Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?" Biomolecules 12, no. 6: 831. https://doi.org/10.3390/biom12060831