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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 Chaudhuri, Debasish and Mulder, Bela and Dekker, Cees (2018) Cell boundary confinement sets the size and position of the E. coli chromosome. . (Submitted) http://resolver.caltech.edu/CaltechAUTHORS:20180823-142905010

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Abstract

While 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 up to 10 times normal, single chromosomes are observed to expand more than 4 fold in size, an effect only modestly influenced by deletions of various nucleoid-associated proteins. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside strictly at mid-cell, while two nucleoids self-organize at 1/4 and 1/4 cell positions. Molecular dynamics simulations of model chromosomes recapitulate these phenomena and indicate that these observations can be attributed to depletion effects induced by cytosolic crowders. These findings highlight boundary confinement as a key causal factor that needs to be considered for understanding chromosome organization.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/348052DOIArticle
ORCID:
AuthorORCID
Wu, Fabai0000-0001-5812-5621
Mulder, Bela0000-0002-8620-5749
Dekker, Cees0000-0001-6273-071X
Additional Information:The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license. bioRxiv preprint first posted online Jun. 15, 2018. We thank Erwin van Rijn, Jeremie Capoulade, Dimitri de Roos, Jelle van der Does, Alexandre Japaridze, Jakub Wiktor, Anne Meyer, and the staff at Kavli NanoLab for technical support and discussions. The work was supported by the Netherlands Organisation for Scientific Research (NWO), the NWO/OCW programs NanoFront and Basyc, and by the European Research Council Advanced Grant SynDiv (No. 669598). D.C.'s work was supported by SERB, India through grant number EMR/2016/001454. Author Contributions: F.W. and C.D. designed the experiments. F.W., L.K., X.Z., K.F., and M.G. did the experiments and analyzed the data. F.W. fabricated the microstructures and wrote the data analysis codes. DC and BM 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. & C.D wrote the paper.
Funders:
Funding AgencyGrant Number
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)UNSPECIFIED
European Research Council (ERC)669598
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
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:23 Aug 2018 21:49

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