The circadian cycle: is the whole greater than the sum of its parts?

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

Temperature compensation in circadian clock models

Circadian clock of organisms has a free-running period that does not change much with ambient temperature. This property "temperature compensation" is studied when the rate of all reaction steps increase with temperature in the biochemical network generating the rhythm. The period becomes shorter when all the rate parameters are enhanced by the same factor. However, the period becomes longer as degradation rate of proteins and/or transcription rate of the clock gene increase (their elasticity is positive). This holds for a wide range of models, including N-variable model, and PER-TIM double oscillator model, provided that (1) branch reactions (e.g. degradation of proteins or mRNAs) are strongly saturated, and that (2) the cooperativity of transcription inhibition by nuclear proteins is not very large. A strong temperature sensitivity of degradation of PER proteins and/or temperature-sensitive alternative splicing of per gene, known for Drosophila, can be mechanisms for the temperature compensation of circadian clock.

Saturation of enzyme kinetics in circadian clock models

From the mathematical study of simple models for circadian rhythm, the authors identified a clear effect of saturation in the enzyme kinetics on the promotion or suppression of a sustained oscillation. In the models, a clock gene (per gene) is transcribed to produce mRNAs, which are translated to produce proteins in the cytosol which are then transported to the nucleus and suppress the transcription of the gene. The negative feedback loop with a long time delay creates sustained oscillation. All the enzymatic reactions (e.g., degradation, translation, and modification) are assumed to be of Michaelis-Menten type. The reaction rate increases with the amount of substrate but saturates when it is very large. The authors prove mathematically that the saturation in any of the reactions included in the feedback loop (in-loop reaction steps) suppresses the oscillation, whereas the saturation of both degradation steps and the back transport of the protein to cytosol (branch reaction steps) makes the oscillation more likely to occur. In the experimental measurements of enzyme kinetics and in published circadian clock simulators, in-loop reaction steps have a small saturation index whereas branch reaction steps have a large saturation index.

Comparative study of circadian clock models, in search of processes promoting oscillation

We study simple models for circadian rhythm, and examine the condition in which the equilibrium is unstable, generating a sustained oscillation. In the models, a clock gene(s) is transcribed to produce mRNAs, which are translated to produce proteins that suppress the transcription of the clock gene(s). First, using a Lyapunov function, we prove under very general conditions that two-variable models cannot generate a stable oscillation, implying that additional structures are needed for the model to generate a sustainable rhythm. By comparing several models of different complexities using the Routh-Hurwitz criteria of stability, we show that a sustained oscillation is more likely to occur if the cell is compartmentalized and the proteins need to be transported from the cytosol to the nucleus, if the proteins have to be modified before entering the nucleus, if the kinetics of transcription inhibition or the transport to the nucleus have cooperativity with a nonlinear dependence on the substrate concentration, or if the products of two clock genes form a heterodimer that suppresses both of their own genes. We discuss the implications of these results.

A fungus among us: the Neurospora crassa circadian system

Neurospora crassa is the only molecular genetic model system for circadian rhythms research in the fungi. Its strengths as a model organism lie in its relative simplicity--compared to photosynthesizing and vertebrate organisms, it is a stripped-down version of life. It forms syncitial hyphae, propagates and reproduces, and the circadian clock is manifest in numerous processes therein. As with other model circadian systems, Neurospora features a transcription/translation feedback loop that is fundamental to an intact circadian system. The molecular components of this loop converge with those of blue light photoreception, thus bringing the clock and one of its input pathways together.

Seasonality and photoperiodism in fungi

This review gives a retrospective of what is known about photoperiodism in fungi, which is largely based on reports about seasonal spore concentrations. Relatively few species have been investigated under laboratory conditions, so that our knowledge whether seasonal reproduction in fungi is mainly a direct response to environmental conditions or whether it involves a photoperiodic machinery with memory capacities and a relationship to the circadian system is extremely limited. To form a basis for further experimental endeavors into fungal photoperiodism, we review the reports about endogenous rhythms and photobiology. Finally, we will look at the possibilities of using the fungal circadian model system of Neurospora crassa for future work on photoperiodism.