Intracellular protein patterns in shape-manipulated E coli cells

8.Rectangles_experiments

Cells are complex architectural units in which substructures hierarchically assemble. The dynamic behavior of these substructures across space and time are constrained by the cell boundary, i.e. the cytoplasmic membrane and the cell wall in the case of bacteria. We investigate how the geometry of cell boundary facilitates and constrains the workings of intracellular components through systematic manipulation of cell shape and size and quantitative analyses of molecular dynamics in these cells. Cell shaping is achieved through various nanofabrication and microfluidic techniques. We currently focus on the spatial organization of cell-division-related components, including the spatial adaptation of Min protein oscillators, chromosomes and cytoskeleton in E. coli. Through these studies, we aim to explore the fundamental biophysics governing the interactions 1) between boundary and Turing reaction-diffusion networks, and 2) between boundary and biopolymers.

In our group, we have found that rod-shape E. coli can ‘squeeze’ through narrow nanoslits much smaller than their regular diameter and change their shape1. This ‘squeezed’ phenotype showed remarkable robustness and accuracy in growth and division, with an equal distribution of chromosome and cytoplasmic content into daughter cells, a feature comparable to the regular rod shape. Further investigation underscored the importance of nucleoid occlusion in the spatial adaptation of division-site selection2.

TUD_improved

Recently, we developed novel techniques to shape living E. coli cells into defined shapes across a large range of scales, making it possible to study the effect of shape and scale systematically and quantitatively3.

1      Männik, J., Driessen, R., Galajda, P., Keymer, J. E. & Dekker, C. Bacterial growth and motility in sub-micron constrictions. Proc. Natl. Acad. Sci. U.S.A. 106, 14861-14866 (2009).

2      Männik, J., Wu, F., Hol, F.J.H., Bisicchia, P., Sherratt, D.J., Keymer, J.E. & Dekker, C.  Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes. Proc. Natl. Acad. Sci. U.S.A. 109, 6957-6962 (2012).

3.     Wu, F., van Schie, B.V.G., Keymer, J.E. & Dekker, C. Symmetry and scale orient Min protein patterns in shaped bacterial sculptures. Nature Nanotechnology. doi:10.1038/nnano.2015.126 (2015)

4.     Wu, F. & Dekker, C. Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology
Chemical Society Reviews (2015)