Department of Molecular Biology Seminar Series: Biophysics studies on the shaping of chromosomes

Department of Molecular Biology Seminar Series

  • Date: Jun 6, 2019
  • Time: 13:00 - 14:00
  • Speaker: Cees Dekker
  • Delft University of Technology
  • Location: Max-Planck-Institut für biophysikalische Chemie (MPIBPC)
  • Room: Tower IV, Seminar Room, 2nd Floor
  • Host: Prof. Dr. Patrick Cramer
  • Contact: office.cramer@mpibpc.mpg.de
Department of Molecular Biology Seminar Series: Biophysics studies on the shaping of chromosomes
I will present some of the recent biophysics studies from our lab that address the spatial structure of chromosomes:

i. Real-time imaging of DNA loop extrusion by condensin [1]
Structural Maintenance of Chromosomes (SMC) proteins have been hypothesized to spatially organize chromosomes by extruding DNA into large loops. Using a single-molecule assay, we provide unambiguous evidence for loop extrusion by directly visualizing the processive extension of DNA loops by yeast condensin in real-time. We find that a single condensin is able to extrude DNA at a force-dependent speed of up to 1,500 base pairs per second, using ATP hydrolysis. Condensin-induced loop extrusion is strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.

ii. Size and position of a single chromosome in a long E. coli cell.
We experimentally show that spatial confinement plays a dominant role in determining both the chromosome size and position [2]. In non-dividing E. coli cells with lengths to 10 times normal, single chromosomes are observed to expand >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 3⁄4 positions. Molecular dynamics simulations with model chromosomes and crowders recapitulate these phenomena and identify depletion effect between cytosolic crowders and the chromosome as the underlying driver of these observations. These findings highlight boundary confinement and crowders as key causal factors that mediates chromosome organization.

iii. Direct imaging of the circular chromosome in a shape-shifted live bacterium.
We exploit cell shaping [3] to enable direct imaging of the circular chromosome in live E. coli bacteria through cell broadening [4]. The chromosome exhibits a torus topology with a 4.2μm toroidal length and 0.4μm bundle thickness. At the single-cell level, the DNA density along the torus is strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. We show that prominent domain boundaries at the terminus and origin of replication are induced by MatP proteins, while weaker transient domain boundaries are facilitated by the global transcription regulators HU and Fis.

[1] M. Ganji et al, Science 360, 102 (2018).
[2] F. Wu et al, Curr. Biol., June 2019, in print, www.biorxiv.org/content/early/2018/06/15/348052
[3] F. Wu et al, Nature Nanotechn. 10, 719 (2015).
[4] F. Wu, A. Japaridze, et al, Nature Commun., May 16, 2019
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