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                     <p>Project Design</p>
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                     <p>PROJECT DESIGN</p>
 
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               Circadian clocks, also know as Circadian oscillators,&nbsp;are ubiquitous timing systems that induce rhythms of biological&nbsp;activities in synchrony with night and day.&nbsp;Circadian oscillators are post-translationally regulated and affect gene expression in autotrophic circadian cyanobacteria.&nbsp;Most work on the cyanobacterial&nbsp;circadian&nbsp;clock has been performed in <em>Synechococcus elongatus</em>&nbsp;PCC&nbsp;7942 (<em>S. elongatus</em>). In <em>S. elongatus</em>&nbsp;7942, timing is generated by a&nbsp;post-translational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output&nbsp;signaling proteins, SasA, RpaA and CikA, which transduce this rhythm to control gene expression&nbsp;and chromosome topology <sup><a href="#re1">1</a></sup>.
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               Circadian clocks, also know as circadian oscillators,&nbsp;are ubiquitous timing systems that induce rhythms of biological&nbsp;activities in synchrony with night and day.&nbsp;Circadian oscillators are post-translationally regulated and affect gene expression in autotrophic circadian cyanobacteria.&nbsp;Most work on the cyanobacterial&nbsp;circadian&nbsp;clock has been performed in <em>Synechococcus elongatus</em>&nbsp;PCC&nbsp;7942 (<em>S. elongatus</em>). In <em>S. elongatus</em>&nbsp;7942, timing is generated by a&nbsp;post-translational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output&nbsp;signaling proteins, SasA, RpaA and CikA, which transduce this rhythm to control gene expression&nbsp;and chromosome topology <sup><a href="#re1">1</a></sup>.
 
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                                       Based on this background knowledge, we designed experiments to couple the regulation of the KaiABC rhythm oscillation system with the S. cerevisiae chromatin topology. It is possible to achieve the regulation of the transcription and expression of global endogenous genes by KaiABC rhythm system in yeast. We choosed chromatin remodeling complex for research.<sup><a href="#re6">6</a></sup>
 
                                       Based on this background knowledge, we designed experiments to couple the regulation of the KaiABC rhythm oscillation system with the S. cerevisiae chromatin topology. It is possible to achieve the regulation of the transcription and expression of global endogenous genes by KaiABC rhythm system in yeast. We choosed chromatin remodeling complex for research.<sup><a href="#re6">6</a></sup>
 
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Latest revision as of 13:00, 6 December 2018

<!DOCTYPE html> Team:Tianjin - 2018.igem.org

PROJECT DESIGN

Circadian clocks, also know as circadian oscillators, are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. Circadian oscillators are post-translationally regulated and affect gene expression in autotrophic circadian cyanobacteria. Most work on the cyanobacterial circadian clock has been performed in Synechococcus elongatus PCC 7942 (S. elongatus). In S. elongatus 7942, timing is generated by a post-translational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA, RpaA and CikA, which transduce this rhythm to control gene expression and chromosome topology 1.

The goal of our project is to reconstruct the KaiABC circadian clock system from prokaryotic cyanobacteria (S. elongatus 7942) in noncircadian eukaryotic Saccharomyces cerevisiae (S. cerevisiae). And we are aim to achieve the controllability of this circadian clock system in Saccharomyces cerevisiae through some practical methods, such as changing the molecular concentration ratio of the core protein KaiA, KaiB and KaiC, which can help us better understand and futher explore the KaiABC system. In addition to the reconstruction of KaiABC, we tried to regulate the metabolic activities of S. cerevisiae using this prokaryotic circadian clock system. What’s more, Our project got a lot of meaningful inspiration from our modeling work. According to the reaction mechanism, a series of rate equations can be obtained. And our modeling work has successfully influenced and corrected our understanding of the KaiABC rhythm system. Click here for more imformation about Modeling.

Some previous research findings have pointed to a possible global regulatory mechanism of the clock through the systematic alteration of chromosome topology2. Although the underlying process are not revealed yet, researchers have identified that S. elongatus PCC 7942 genes exhibit circadian fluctuations and that these changes are highly correlated with rhythmic changes in the superhelical density of the chromosome3. Inspired by these studies, we expect that the S. cerevisiae chromasome topology will periodically oscillate with the KaiABC circadian clock system.

In addition to understanding and exploring basic biological science through construction and building, we also explored applications of this circadian clock system in S. cerevisiae. The novel application we envisioned was that S. cerevisiae can produce different products alternately under the periodic regulation of the KaiABC circadian clock.

1. Reconstruction of KaiABC circadian clock with different strategies
2. Design of gene circuits and output of oscillating signals
3. Regulation of introduced prokaryotic clock systems in eukaryotic cells
4. Prokaryotic clock system regulates eukaryotic yeast by periodically affecting the topology of eukaryotic chromatin
5. Novel applications

References

[1]Tseng, R. et al. Structural basis of the day-night transition in a bacterial circadian clock. Science 355, 1174-1180, doi:10.1126/science.aag2516 (2017).

[2]Shultzaberger, R. K., Boyd, J. S., Diamond, S., Greenspan, R. J. & Golden, S. S. Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context. Annu Rev Genet 49, 485-505, doi:10.1146/annurev-genet-111212-133227 (2015).

[3]Woelfle, M. A., Xu, Y., Qin, X. & Johnson, C. H. Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc Natl Acad Sci U S A 104, 18819-18824, doi:10.1073/pnas.0706069104 (2007).

[4]Kageyama, H. et al. Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro. Mol Cell 23, 161-171, doi:10.1016/j.molcel.2006.05.039 (2006).

[5]Terauchi, K. et al. ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. P Natl Acad Sci USA 104, 16377-16381, doi:10.1073/pnas.0706292104 (2007).

[6]Narlikar, G. J., Fan, H. Y. & Kingston, R. E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475-487, doi:Doi 10.1016/S0092-8674(02)00654-2 (2002).

[7]Rust, M. J., Golden, S. S. & O'Shea, E. K. Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator. Science 331, 220-223, doi:10.1126/science.1197243 (2011).