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Direct Imaging of the circular chromosome of a live bacterium

Wu, Fabai and Japaridze, Aleksandre and Zheng, Xuan and Wiktor, Jakub and Kerssemakers, Jacob W. J. and Dekker, Cees (2019) Direct Imaging of the circular chromosome of a live bacterium. Nature Communications, 10 . Art. No. 2194. ISSN 2041-1723. PMCID PMC6522522. doi:10.1038/s41467-019-10221-0.

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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.

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URLURL TypeDescription CentralArticle Paper
Wu, Fabai0000-0001-5812-5621
Japaridze, Aleksandre0000-0002-9581-9128
Dekker, Cees0000-0001-6273-071X
Additional Information:© 2019 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit Received 27 August 2018; Accepted 26 April 2019; Published 16 May 2019. Data availability: The data underlying Figs. 1, 2, 3e and 3f are provided as a Source Data file. Datasets that were acquired and analysed during the current study are available from the corresponding author upon request. Code availability: The analysis codes that were used in the current study are available from the corresponding author upon request. We thank Jeremie Capoulade, Erwin van Rijn, Jelle van der Does, Louis Kuijpers, My Nguyen, Margot Guurink, and Linda Chen (Huygens) for technical assistance, and David Sherratt, Rodrigo Reyes-Lamothe, and Jean-Luc Ferat for bacterial strains. This work was supported by ERC Advanced Grant SynDiv (No. 669598) and the Netherlands Organization of Scientific Research (NWO/OCW) as part of the Frontiers of Nanoscience Program. F.W. acknowledges support by Rubicon fellowship. A.J. acknowledges support by the Swiss National Science Foundation (Grants P2ELP2_168554 and P300P2_177768). Author Contributions: F.W. and C.D. conceived and designed the project. F.W., A.J., and J.W. constructed the bacterial strains. F.W., A.J., J.W., and X.Z. did the microscopy experiments. A.J. performed the bacterial growth experiments. J.W.J.K. led the image analyses. J.W.J.K., F.W., and X.Z. wrote the data analysis programs. All authors wrote the paper. C.D. supervised the project. The authors declare no competing interests.
Funding AgencyGrant Number
European Research Council (ERC)669598
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)UNSPECIFIED
Swiss National Science Foundation (SNSF)P2ELP2_168554
Swiss National Science Foundation (SNSF)P300P2_177768
PubMed Central ID:PMC6522522
Record Number:CaltechAUTHORS:20181031-092728968
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90538
Deposited By: Tony Diaz
Deposited On:01 Nov 2018 18:17
Last Modified:25 Feb 2022 17:25

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