The project has been split into categories:
Together, this forms the UQ-Australia project for the 2011 iGEM.
In humans, the circadian rhythm is controlled by several core genes that operate via a series of feedback loops (Figure 1). A transcription–translation negative-feedback loop powers the system, with a delay between the transcription of these genes and the negative feedback being a key factor that allows the system to oscillate [1]. A 'master clock' located in the Suprachiasmatic Nucleus coordinates the timing of the rhythm, but external factors such as light exposure play a large role in regulating the exact
Figure 1: The gene network responsible for establishing the circadian rhythm in humans [1]
There has been much effort put into reconstructing and determining the exact nature of this system, as the impact the circadian rhythm has on our lifestyle and cellular processes are still not very well understood. In particular, it is believed the circadian rhythm could exert an effect on everything from body temperature, feeding behaviour and appetite, hormone secretion and metabolism, glucose homeostasis, and cell-cycle progression [2].
Consequently, there have been a number of efforts to reconstruct this clock in a mammalian system for further study. In particular, both Hong et al. [3] and Tigges et al. [4] utilize the inducible tTa system to drive the expression and oscillation of genes in their synthetic networks.
It was our initial plan to construct a similar oscillatory system ourselves using standardized parts which could be added to the registry and then utilized by other iGEM teams working in mammalian cells. Such as system could be 'plugged in' to any number of different outputs and would allow for the timely and regular expression of the genes it drives. However, we encountered a number of issues around the intellectual property protecting of certain elements we wanted to use and so decided to switch to a simpler system in E. coli.
In prokaryotic systems, there are a number of tools available for synthetic biologists to construct gene networks such as the circadian clock we hope to replicate. In particular, we are going to make use of the inducible promoters glnAp2 and pBAD and their inducers glnG and araC. These components have been used in synthetic oscillators from both Atkinson et al. [5] and Stricker et al. [6]. In addition, we plan on using an engineered promoter denoted as Plac/ara, which features a pBAD activation domain as well as several lacO sites, meaning it is both inducible and repressible depending on the input. This promoter was first engineered by Lutz & Bujard [7].
Based on the work from these previous studies, we designed our own system using components that have been previously utilized to construct other synthetic clocks (Figure 2). We decided to make a 3 component system rather that a dual component system as the issues encountered by some other synthetic clocks suggest that there might not have been enough time between the transcription of various components [8]. As such, including this extra step to add a delay should ensure our network is able to reach an oscillatory expression pattern.
Figure 2: The genetic system we are aiming to construct in order to produce an oscillating gene network.
Details of this is on the Modelling page.
Details of this is on the Safety page.
The Human Practices section is on the Human Practices
[1] Gallego, M & Virshup, DM 2007. "Post-translational modifications regulate the ticking of the circadian clock", Molecular Cell Biology, vol. 8, pp. 139-148.
[2] Takahashi, JS, Hong, HK, Ko, CH & McDearmon, EL 2008. "The genetics of mammalian circadian order and disorder: implications for physiology and disease", Genetics, vol. 9, pp. 764-775.
[3] Hong, HK, Chong, JL, Song, W, Song, EJ & Jyawook, AA et al. 2007. "Inducible and reversible Clock gene expression in brain using the tTa system for the study of circadian behaviour", PLoS Genetics, vol. 3, no. 2, 324-338.
[4] Tigges, M, Marques-Lago, TT, Stelling, J & Fusseneger, M 2009. "A tunable synthetic mammalian oscillator", Nature, vol. 457, pp. 309-312.
[5] Atkinson, MR, Savageau, MA, Myers, JT & Ninfa, AJ 2003. "Development of genetic circuitry exhibiting toggle switch or oscillatory behaviour in Escherichia coli", Cell, vol. 113, pp. 597-607.
[6] Stricker, J, Cookson, S, Bennett, MR, Mather, WH, Tsimring, LS & Hasty, J 2008. "A fast, robust and tunable synthetic oscillator", Nature, vol. 456, pp. 516-520.
[7] Lutz, R & Bujard H 1997. "Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and araC/I1-I2 regulatory elements", Nucleic Acids Research, vol. 25, no. 6, pp. 1203-1210.
[8] Purcell, O, Savery, NJ, Grierson, CS & di Bernardo, M 2010. "A comparative analysis of synthetic genetic oscillators", Journal of the Royal Society, vol. 7, pp. 1503-1524.