Direct imaging of the circular chromosome in a live bacterium

Fabai Wu,Cees Dekker,Jacob W J Kerssemakers,Jakub Wiktor,Xuan Zheng,Aleksandre Japaridze

doi:10.1038/s41467-019-10221-0

Fabai Wu, Cees Dekker + Show 4 more

Open Access

https://doi.org/10.1038/s41467-019-10221-0

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Abstract

Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower-density origin of replication and an ultrathin flexible string of DNA at the terminus of replication. At the single-cell level, the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells.

Highlights

The physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved
Upon treatment for a short time with drugs such as rifampicin or ciprofloxacin, or upon induction of the stationary phase, the chromosomes collapsed and generally lost the torus topology (Supplementary Fig. 6A)
The torus topology was not dependent on the slightly elevated temperature (40 °C) used to maintain a single chromosome in the cells, nor was it unique to the AB1157 strain used in the experiments

Summary

Introduction

The physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Our data show a domain organization underlying the chromosome structure of E. coli, where MatP proteins induce site-specific persistent domain boundaries at Ori/Ter, while transcription regulators HU and Fis induce weaker transient domain boundaries throughout the genome. These findings provide an architectural basis for the understanding of the dynamic spatial organization of bacterial genomes in live cells. The vast majority (>80%) of cells maintained only one single chromosome while growing from a rod into a lemon shape (~2-μm wide, ~4-μm long, and ~1-μm high under an agarose pad) over the course of 2–3 h (Fig. 1b)

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