Bioorthogonal circadian clocks

Introduction
Circadian rhythms are essential adaptive measures organisms take to match metabolic processes to predictable environmental fluctuations. Investigations into circadian clocks have provided much insight, yet more research is necessary to understand some fundamental aspects of the mechanisms at work, especially for applications in synthetic biology. Once wholly understood and modelled, such systems can prove valuable tools in both industry (offering temporal control over various metabolic cellular processes) and academia (a basis for research into the complex eukaryotic homologues).

The simplest authentic clock is found in cyanobacteria. Its central oscillator of the circadian clock has been reproduced in vitro, using only the core proteins (KaiA, KaiB and KaiC) and ATP as a source of energy. More recent work has achieved transplantation of this central oscillator into E. coli, a noncircadian organism. These achievements make great progress in understanding the core oscillating elements of circadian clocks and show the feasibility of transplantation, yet in previous work did not produce stable oscillations in vivo. Also, little attention is given to the information output pathway, through which temporal data is communicated by the central oscillator to the machinery of the cell.

Aims
Based on research showing a functional central oscillator in vitro, the aim of the project is reproducing the set-up and adding to it an output pathway.

This would be achieved by reconstituting the central oscillator in vitro: Kai, KaiB and KaiC + ATP. Output proteins would be used to transmit information from the central oscillator to a gene found under the transcriptional control of said output proteins. A successful experiment would yield rhythmic transcription of the gene (generating mRNA), and would be comparable to the rhythmic phosphorylation of KaiC.

The project is part of the Portabolomics initiative, aiming to generate a synthetic bio-adaptor that will serve as a standardised interface to the cell's essential biological processes. In vitro generated parameters will be fed into the Portabolomics computer models.

The project is based in the newly built Baddiley-Clark building, at the Centre for Bacterial and Cellular Biology (CBCB), equipped with state-of-the-art instruments including super-resolution microscopy facilities.