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Sci Rep. 2015 Dec 14;5:18146. doi: 10.1038/srep18146.

Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF.

Lee SY1,2,3, Lim CJ2,3, Dröge P4, Yan J1,2,3,5.

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Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.
Department of Physics, National University of Singapore, Singapore 117551, Singapore.
Center for Bioimaging Sciences, National University of Singapore, Singapore 117557, Singapore.
Division of Molecular Genetic and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore.


The bacterial nucleoid, a bacterial genome packed by nucleoid binding proteins, forms the physical basis for cellular processes such as gene transcription and DNA replication. Bacteria need to dynamically modulate their nucleoid structures at different growth phases and in response to environmental changes. At the nutrients deficient stationary phase, DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) are the two most abundant nucleoid associated proteins in E. coli. Yet, it remains unclear how the nucleoid architecture is controlled by the interplay between these two proteins, as well as the nucleoid's response to environmental changes. This question is addressed here using single DNA manipulation approach. Our results reveal that the two proteins are differentially selected for DNA binding, which can be tuned by changing environmental factors over physiological ranges including KCl (50-300 mM), MgCl2 (0-10 mM), pH (6.5-8.5) and temperature (23-37 °C). Increasing pH and MgCl2 concentrations switch from Dps-binding to IHF-binding. Stable Dps-DNA and IHF-DNA complexes are insensitive to temperature changes for the range tested. The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture.

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