The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid

• Published in: Molecular microbiology 2020-05, Vol.113 (5), p.1022-1037
• Main Authors: Yang, Da, Männik, Jaana, Retterer, Scott T., Männik, Jaan
• Format: Article
• Language: English
• Subjects: Cell membranes; Cell Nucleus; Chromatin - metabolism; chromosomal organization; Chromosomes; Chromosomes, Bacterial - genetics; Compacting; Compaction; Compressibility; Deoxyribonucleic acid; DNA; DNA, Bacterial - genetics; DNA-Binding Proteins - physiology; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - growth & development; Escherichia coli Proteins - physiology; Growth rate; macromolecular crowders; Macromolecules; Nucleic Acid Synthesis Inhibitors - pharmacology; nucleoid; Organelles - physiology; Osmotic Pressure; Osmotic shock; Polyribosomes - physiology; Proteins; Ribosomes; Rifampin; Rifampin - pharmacology; Supercoiling
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.14467

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. The bacterial chromosome is compacted into a distinct organelle‐like entity termed the nucleoid, which occupies about one half of the cytosolic volume. Our studies of Escherichia coli cells using osmotic and mechanical shocks show that the main contribution to the formation of the nucleoid comes from the macromolecular crowders in the cytoplasm. The main crowder species responsible for chromosome compaction are soluble cytoplasmic proteins and poly ribosomes.