A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation
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- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
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- Document Type:
- Manuscript
- Date:
- Received 09 October 2009 08:58 UTC; Posted 09 October 2009
- Subjects:
- Developmental Biology, Microbiology, Bioinformatics
- Abstract:
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally.
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- This document is licensed to the public under the Creative Commons Attribution 3.0 License
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Arjunan, Satya and Tomita, Masaru. A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3845.1> (2009)
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Satya Arjunan on 09 October 2009 10:15 UTC
Video S1 in the manuscript can be viewed here:
http://www.scivee.tv/node/12912
Any comments about the manuscript is highly appreciated.