3D model of a bacterial division machinery

A very first modelling of the bacterial septosome. The 3D scene can be downloaded from the Download section.

Authors :

  • D.Larivière, E.Fourmentin (Fondation Fourmentin-Guilbert), O. Mavré (LISAA)
  • N. Dubarry, M.-L. Bonné, F.-X. Barre (Centre de Génétique Moléculaire, CNRS, Gif/Yvette)
In E. coli, at least 11 proteins are known to participate in the division process : FtsZ, ZipA, FtsA, ZapA, FtsK, FtsQ, FtsL, FtsB, FtsW, FtsI, FtsN. An early step in bacterial cytokinesis is the formation of a FtsZ ring like structure at the site of septation, which contracts as the cell divides. Strucural and microscopic studies led to the proposal that FtsZ may function as a cytoskeletal element in prokaryotes, analogous to tubulin in eukaryotes.

 

Before cell contraction, FtsA, ZipA, ZapA and FtsK are recruited at the FtsZ ring. FtsA, ZipA and ZapA have been shown to interact with FtsZ, to drive its polymerisation and to promote FtsZ filament bundling thereby contributing to the spatio-temporal tuning of the Z-ring. Additionnal functions of FtsA and ZipA may be to link the membrane with the FtsZ rings in order to stabilize or organize the rings. FtsK is a DNA translocase that coordinates chromosome segregation and cell division in bacteria. In addition to its role as activator of XerCD site-specific recombination, FtsK can translocate double-stranded DNA rapidly and directionally and reverse direction. Finally, FtsA and FtsK seem to interact with and target other division proteins and their lack results in a cell unable to contract. Picture 1 shows two microscopy images of a dividing E.coli cell : the large one in red, obtained by Christian Lesterlin (CGM-CNRS, Gif), clearly shows DNA (stained by DAPI) trapped at the septum ; the small one, obtained by Nelly Dubarry, shows a wild-type E. coli cell observed by differential-interference microscopy.

picture2

Pictures 2 to 4 shows a very first model of the septosome in the final stage of the division process and created with the LifeExplorer software. This model includes 177 proteins : 2 double-rings with 96 FtsZ proteins (in yellow), 51 FtsA proteins (in dark blue), 6 ZipA Cter (in red), 10 ZapA tetramer bridging two FtsZ rings, 2 FtsK hexamer (Cter : 6  alpha, beta and gamma domains). Only one portion of DNA is shown. This 678 DNA bp has been created using DNA tools of The International Center for Genetic Engineering and Biotechnology (ICGEB) in Trieste (Vlahovicek K, Kajan L, Pongor S. DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res. 2003 Jul 1;31(13):3686-7. PMID: 12824394). All proteins has been created from their PDB structure using the UCSF Chimera Multiscale models tool generating low-resolution surfaces (T.D. Goddard, C.C. Huang, and T.E. Ferrin, “Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies” Structure 13:473 (2005). PMID: 15766548). FtsZ : PDB 2VAW; FtsA : PDB 1E4F; ZipA : PDB 1F7W; ZapA tetramer : PDB 1W2E; FtsK hexamer : PDB 2IUU; Gamma domain : PDB 2J5P Next steps : Insertion of membranar proteins; modelling of XerCD site-specific recombination; modelling of FtsZ-ring formation; insertion of more FtsK motors under the form of monomers and hexamer; insertion of one supplementary portion of DNA; …

References :

  • W. Margolin, “FtsZ and the division of prokaryotic cells and organelles”, Nature Reviews Molecular Cell Biology 6, 2005
  • Bigot et al, “FtsK, a literate chromosome segregation machine”, Molecular Microbiology 64 (6), 2007
  • T. H. Massey et al, “Double-Stranded DNA Translocation: Structure and Mechanism of Hexameric FtsK”, Molecular Cell 23, 2006
  • M.A. Oliva et al, “Structural insights into FtsZ protofilament formation”, Nature Structural and Molecular Biology 11, 2004
  • A. Vendeville et al, “An inventory of the bacterial macromolecular components and their spatial organization”, FEMS Microbiology Reviews 35 (2), 2011