Robust circadian clocks from coupled protein modification and transcription-translation cycles

TL;DR

This study shows that robust circadian rhythms in cyanobacteria require the interaction of both protein modification and transcription-translation cycles, especially under varying growth conditions, with each cycle compensating for the limitations of the other.

Contribution

It demonstrates through stochastic simulations that coupled protein modification and transcription-translation cycles are essential for stable circadian rhythms across different growth rates.

Findings

Protein phosphorylation cycle alone is robust at low decay rates.

High decay rates impair phosphorylation-based oscillators.

Both cycles are necessary for robustness across growth conditions.

Abstract

The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription-translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to analyze how these cycles interact to generate stable rhythms in growing, dividing cells. We find that a protein phosphorylation cycle by itself is robust when protein turnover is low. For high decay or dilution rates (and co mpensating synthesis rate), however, the phosphorylation-based oscillator loses its integrity. Circadian rhythms thus cannot be generated with a phosphorylation cycle alone when the growth rate, and consequently the rate of protein dilution, is high enough; in practice, a purely post-translational clock ceases to function well when the cell doubling time drops below the 24 hour clock period. At higher growth rates, a transcription-translation cycle becomes essential for generating robust circadian rhythms. Interestingly, while a transcription-translation cycle is necessary to sustain a phosphorylation cycle at high growth rates, a phosphorylation cycle can dramatically enhance the robustness of a transcription-translation cycle at lower protein decay or dilution rates. Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.