Abstract
DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle-like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a three-fold decrease in the nucleoid's volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels, the nucleoid becomes spherical, and its compressibility decreases significantly. Furthermore, we find that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid. The contribution of poly ribosomes dominates at faster and soluble proteins at slower growth rates.
| Original language | English |
|---|---|
| Pages (from-to) | 1022-1037 |
| Number of pages | 16 |
| Journal | Molecular Microbiology |
| Volume | 113 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 1 2020 |
Funding
The authors thank Fabai Wu, Cees Dekker and Rodrigo Reyes‐Lamothe for strains and plasmids, and Sriram Tiruvadi Krishnan, Bryant E. Walker, Conrad L. Woldringh and Arieh Zaritsky for valuable comments. Authors acknowledge technical assistance and material support from the Center for Environmental Biotechnology at the University of Tennessee. This work was supported by National Science Foundation research grant [MCB‐1252890], US‐Israel Binational Science Foundation research grant [2017004], and National Institutes of Health award under [R01GM127413]. Part of this research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. A part of this research is based upon work performed using computational resources supported by the University of Tennessee and Oak Ridge National Laboratory Joint Institute for Computational Sciences. The authors thank Fabai Wu, Cees Dekker and Rodrigo Reyes-Lamothe for strains and plasmids, and Sriram Tiruvadi Krishnan, Bryant E. Walker, Conrad L. Woldringh and Arieh Zaritsky for valuable comments. Authors acknowledge technical assistance and material support from the Center for Environmental Biotechnology at the University of Tennessee. This work was supported by National Science Foundation research grant [MCB-1252890], US-Israel Binational Science Foundation research grant [2017004], and National Institutes of Health award under [R01GM127413]. Part of this research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. A part of this research is based upon work performed using computational resources supported by the University of Tennessee and Oak Ridge National Laboratory Joint Institute for Computational Sciences.
Keywords
- DNA
- Escherichia coli
- chromosomal organization
- macromolecular crowders
- nucleoid
- osmotic shock