Biology in the context of boundary: Genome organization and Pattern formation

  • Speaker:           Fabai Wu
  • Department:     BioNanoScience
  • Subject:            Biology in the context of boundary: Genome organization and pattern formation
  • Location:          TU Delft
  • Date:                11-05-2016
  • Author:             Katja Slangewal

Fabai Wu starts his talk with the plant Brunsvigia, which lives in the dry areas of Africa. When, after several years, the rain starts falling, the plant starts growing and its branch breaks of the roots. Because of the spherical shape, the plant starts rolling in the wind until its seeds can grow new plants far away. Wu wonders why there are almost no animals using a rolling strategy instead of walking. Clear is that walking appeared evolutionary preferable over rolling. This can be traced back to the complex interaction between the genotype and the phenotype. The development from a relatively simple embryo to a complex organism lies within these interactions.  The appearance of asymmetry for instance depends on the interaction of several chemicals. Even the simplest cases with two chemicals can form patterns. Wu is interested in these self-organized patterns and in the regulation of the transfer of information between genotype and phenotype. A better understanding of these processes will lead to a better understanding of the emergence of life. Today, he tells more about self-organized patterns and genome organization in the boundary of biology.

seminar 5 dna

Figure 1: E. coli DNA needs extra forces to fit into the small cells. [1]

Wu has been using E. coli and its Min system to learn more about genome organization and self-organized patterns. The usual day of an E. coli bacterium exists of growing and dividing over and over
again. To have an idea of the size: an E. coli bacterium is on average 2-6μm long and it has a diameter of 1μm. Its genome consists of 4,6Mbp and if it were stretched out, it would be 1,5m long. To fit this large molecule into the small bacterium extra forces are needed. The question was, whether these forces mainly come from intra-nucleoid interactions or from boundary constraints. So far, it is not possible to see the DNA structure within E. coli with imaging techniques.  This was solved by making more space in the bacterium. The genes encoding for division were knocked out so that E. coli cannot divide. Also, they made sure that the cell lost its rod-shape. After approximately 1,5 hour the bacteria had grown enough to see the circular shape of the DNA. This showed that the chromosome is pushed to a helical form due to a small cell-width.

Next, E. coli was allowed to grow only in one direction. This maintained the rod-shape of the bacterium. The DNA was not allowed to divide. Wu found that until a certain point the DNA does not expand further, although the bacteria are still growing.  After knocking down Fis, a protein able to link different parts of the genome together, the DNA was able to expand further than the wild-type. This suggests the boundary constraints are not the only important forces for fitting the genome into the small bacteria, also nucleoid interactions play a role.

Finally Wu talked about self-organized patterns. The Min system is an oscillating system which prevents the Z ring for forming outside mid-cell. In 30 seconds the Min proteins travel from pole to pole. Wu made nanostructures in different forms, like squares, triangles and circles. The structures were filled with E. coli bacteria that were not able to divide, so they could occupy the entire area. They looked at the Min oscillations in all the forms. They also looked at the same experiment at different scales. It appeared that the Min system searches for a symmetry axis. First it was thought this should be the longest axis, because this is the case in E. coli. However, the experiment showed that the Min system also oscillated around the shortest axis in some cases. The similarity between all the axes is the length. The E. coli Min system prefers a symmetry axis between 3 and 6μm. This agrees with the length E. coli. Wu and his team were also able to effectively predict the experiments with computational models. So to conclude: biology works through self-organization, both in genome organization and pattern formation.
seminar 5 min

Figure 2: The oscillating Min system in different shapes. Left, the shapes are shown. Then, some snap-shots at different time points are shown. Next, the average intensity is visible. The green arrows show the symmetry axis. And on the right all the axes of each shape are shown. [2]

Fabai Wu gave an interesting talk. First I didn’t grasp the subject. The story about the Brunsvigia plant was also interesting, I didn’t know this survival tactic yet, but I found it hard to see the link between the plant and the Min system in E. coli. The rest of the story was quite nice. He explained clearly the results and reasoning behind the conclusions. I already read the article Wu and his colleges wrote about the oscillations of the Min system in different shapes, since my Honours Project is also about the Min system. So my background knowledge for this talk was quite good. Sometimes this was a shame because he was telling a lot of things I already knew. But it was nice to hear about the process behind an article as well. This gave the article an extra dimension.

[1] Griswold, A. (2008) Genome packaging in prokaryotes: the circular chromosome of E. coli. Nature Education 1(1):57.

[2] Wu, F., van Schie, B.G.C, Keymer, J.E., Dekker, C. (2015) Symmetry and scale orient Min protein patterns in shaped bacterial sculptures. Nature nanotechnology. 10: 719-726.

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