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Polymer Physics for Understanding Bacterial Chromosomes

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Bacterial Chromatin

Abstract

This chapter presents polymer physics that is relevant for an understanding of bacterial chromosome segregation. I first show that polymers have a natural tendency for segregation, which can be very strong in the presence of confinement. I then discuss segregation of duplicating chromosomes using the concentric-shell model, which predicts that newly synthesized DNA will be found in the periphery of the chromosome during replication. I sketch implications of these results, e.g., on the role of proteins, segregation mechanisms for bacteria of diverse shapes, cell cycle of an artificial cell, and evolution. Finally, I remind the reader of the robust nature of the bacterial cell cycle by presenting experimental results of Escherichia coli growing in a nano-fabricated slab of thickness under 300 nm.

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Notes

  1. 1.

     For a physical approach to eukaryotic chromosomes, the reader is encouraged to read Marko and Siggia (1997).

  2. 2.

     Note that polymer physics was still in its infancy during Schrödinger’s time. For instance, Flory’s magnum opus, Principles of Polymer Chemistry (1953), appeared almost 10 years after What is Life? (1944).

  3. 3.

     There is an ongoing debate about how long the duplicated ori and other loci stay together before splitting during chromosome segregation (“cohesion”). See, for example, Bates and Kleckner (2005), Nanninga et al. (2002), Nielsen et al. (2006), Sunako et al. (2001).

  4. 4.

     In our previous study (Jun and Mulder 2006), this gap was even smaller than the width of the chain in our simulations.

  5. 5.

     The origin of this result is due to the form of the free energy in Eq. 6.3 (Grosberg et al. 1982; Jun et al. 2007; Sakaue and Raphaël 2006), which has been constructed to be a function of only the monomer density. In other words, regardless of the shape of the envelope surrounding the chains, the free energies will be the same as long as the volumes are also the same, and vice versa. Additional consideration of the interactions at the surface will change the envelope shape, but not segregation/mixing.

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Acknowledgments

I thank A. Arnold, B.-Y. Ha and B. Mulder for many of the collaborative results presented in this book chapter, and W. Dang and P. Galajda for their work mentioned in Fig. 6.10 during their stay in my lab. I am particularly grateful to C. Woldringh for numerous discussions, inspiring conversations and long-term collaborations.

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Authors and Affiliations

  1. FAS Center for Systems Biology, Harvard University, 52 Oxford St, Cambridge, MA, 02138, USA

    Suckjoon Jun

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  1. Suckjoon Jun
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Editors and Affiliations

  1. Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, Netherlands

    Remus T. Dame (Faculty of Mathematics and Natural Sciences) (Faculty of Mathematics and Natural Sciences)

  2. Division of Physics and Astronomy Section Physics of Complex Systems, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands

    Remus T. Dame (Faculty of Mathematics and Natural Sciences) (Faculty of Mathematics and Natural Sciences)

  3. Department of Microbiology School of Genetics and Microbiology, University of Dublin Trinity College, Dublin 2, Ireland

    Charles J. Dorman

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Jun, S. (2010). Polymer Physics for Understanding Bacterial Chromosomes. In: Dame, R.T., Dorman, C.J. (eds) Bacterial Chromatin. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3473-1_6

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