Team:HZAU-China/Description

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Description The chromosome replication of bacteria can be divided into three phases: B C and D $^{[1-3]}$ , and meanwhile multi-rounds of replication exist simultaneously in one cell $^{[1]}$ . So both the replication phase and the copy number of chromosome are heterogeneous in a culture.

To know more about replication

The replication process of E. coli can be divided into three phases; phase B, phase C and phase D. Phase B is also called pre-replication phase, in which cells are preparing for DNA replication, like G1 phase of eukaryotes. Phase C is also called replication phase, in which the genome is under replication, corresponding to phase S in eukaryotic cell cycle. The last phase D, of course, is called post-replication phase, in which chromosome separates and one cell divides into two, corresponding to G2 and M phases in eukaryotes. Among the three phases, C and D are relatively constant, about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle. Recent work revealed a relationship between replication initiation and cell volume, but many details still remain unknown. What we know is that a protein, DnaA, plays an important role in this process. DnaA is a versatile protein possessing many different functions related to cell cycle, among which the most important one is to attach to the OriC, the origins of chromosome replication, and initiates replication. So controlling cell cycle by interrupting the attachment of DnaA and the corresponding DNA sequence with dCas9 is an efficient approach.
The whole cell cycles of eukaryotes and prokaryotes show a certain similarity, but there is difference between them. The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before the last replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown that even an isogenic bacteria growing in the same culture show differences in both replication phase and genome copy numbers and this becomes a huge noise when constructing the 3D genome structure and building up a circuit related to genome . Besides, the development of synthetic biology requires a system to control the reproduction of engineered organisms. So we believe that our project would be a useful tool no matter in theoretical areas or application areas.

Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a 4D genome project of prokaryote. After investigation we find that due to the complicated mechanisms of bacteria chromosome replication, there will be a huge noise while detecting its chromosome structure, which hinders the research on prokaryotic 4D genome $^{[4]}$ . Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation, antidrug resistance research and synthetic biology $^{[5-7]}$ . Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon that can change the traditional opinions? In our mind, the ideal synchronization methods should not only simply inhibit the cell cycle but at the same time can free the inhibition according to our requirements. As we all know, the manipulation of machine is much more accurate than living beings, and there is a trend to let machine help us to control the organisms, so we want our synchronization system can also be controlled by machine and program.

References 1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968 Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5. 2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry. J Bacteriol. 1983 May;154(2) 656-662. 3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2), 252-264. 4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia coli with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990). 5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population. Nature Genetics. 49. . 10.1038/ng.3915.