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Cell boundary confinement sets the size and position of the E. coli chromosome

Wu, Fabai and Swain, Pinaki and Kuijpers, Louis and Zheng, Xuan and Felter, Kevin and Guurink, Margot and Solari, Jacopo and Jun, Suckjoon and Shimizu, Thomas S. and Chaudhuri, Debasish and Mulder, Bela and Dekker, Cees (2019) Cell boundary confinement sets the size and position of the E. coli chromosome. Current Biology, 29 (13). pp. 2131-2144. ISSN 0960-9822. http://resolver.caltech.edu/CaltechAUTHORS:20180823-142905010

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Abstract

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths increased to 10 times normal, single chromosomes are observed to expand > 4-fold in size. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside robustly at mid-cell, whereas two nucleoids self-organize at 1/4 and 3/4 positions. The cell-size-dependent expansion of the nucleoid is only modestly influenced by deletions of nucleoid-associated proteins, whereas osmotic manipulation experiments reveal a prominent role of molecular crowding. Molecular dynamics simulations with model chromosomes and crowders recapitulate the observed phenomena and highlight the role of entropic effects caused by confinement and molecular crowding in the spatial organization of the chromosome.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.cub.2019.05.015DOIArticle
https://doi.org/10.1101/348052DOIDiscussion Paper
ORCID:
AuthorORCID
Wu, Fabai0000-0001-5812-5621
Mulder, Bela0000-0002-8620-5749
Dekker, Cees0000-0001-6273-071X
Additional Information:© 2019 Published by Elsevier Ltd. Received 12 April 2019, Revised 27 April 2019, Accepted 3 May 2019, Available online 30 May 2019. We thank Erwin van Rijn, Jeremie Capoulade, Jelle van der Does, Dimitri de Roos, and the staff at Kavli NanoLab for technical support, and Anne Meyer and Aleksandre Japaridze for discussions. We thank members of Jun lab (UCSD) for help with the osmotic shock experiments, including Steven Brown for strain SJ540 and SJ545 and Sarah Cox for TSS1961. The work was supported by the Netherlands Organization for Scientific Research (NWO), the NWO/OCW programs NanoFront and Basyc, by the European Research Council Advanced Grant SynDiv (No. 669598), NSF CAREER grant MCB-1253843 and NIH grant R01 GM118565-01 to S.J. DC’s work was supported by SERB, India through grant EMR/2016/001454. Author contributions: F.W. and C.D. designed the experiments. FW fabricated the microstructures and wrote the data analysis codes. F.W., L.K., X.Z., K.F., and M.G. did the experiments and analyzed the data. J.S. performed the osmotic shock experiments under the supervision of S.J. and T.S.S. D.C. and B.M. designed the simulations. P.S. performed the simulations under the supervision of D.C. C.D. supervised the experimental work. B.M. supervised the theoretical work. F.W., D.C., B.M., and C.D. wrote the paper. The authors declare no competing interests
Funders:
Funding AgencyGrant Number
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)UNSPECIFIED
European Research Council (ERC)669598
NSFMCB-1253843
NIHR01 GM118565-01
Science and Engineering Research Board (SERB)EMR/2016/001454
Subject Keywords:Bacterial nucleoid; chromosome size; chromosome segregation; cell boundary confinement
Record Number:CaltechAUTHORS:20180823-142905010
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20180823-142905010
Official Citation:Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mulder, Cees Dekker, Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome, Current Biology, Volume 29, Issue 13, 2019, Pages 2131-2144.e4, ISSN 0960-9822, https://doi.org/10.1016/j.cub.2019.05.015. (http://www.sciencedirect.com/science/article/pii/S0960982219305482)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:89097
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:23 Aug 2018 21:49
Last Modified:10 Jul 2019 16:43

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