Cost-effective circadian mechanism: rhythmic degradation of circadian proteins spontaneously emerges without rhythmic post-translational regulation

Generalized Michaelis-Menten rate law with time-varying molecular concentrations

The Michaelis-Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry, biophysics, cell biology, systems biology, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than the molecular concentrations change. Yet, this assumption is not always justified. Here, we relax this quasi-steady state requirement and propose the generalized MM rate law for the interactions of molecules with active concentration changes over time. Our approach for time-varying molecular concentrations, termed the effective time-delay scheme (ETS), is based on rigorously estimated time-delay effects in molecular complex formation. With particularly marked improvements in protein-protein and protein-DNA interaction modeling, the ETS provides an analytical framework to interpret and predict rich transient or rhythmic dynamics (such as autogenously-regulated cellular adaptation and circadian protein turnover), which goes beyond the quasi-steady state assumption.

A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules

Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.

Backward simulation for inferring hidden biomolecular kinetic profiles

Our backward simulation (BS) is an approach to infer the dynamics of individual components in ordinary differential equation (ODE) models, given the information on relatively downstream components or their sums. Here, we demonstrate the use of BS to infer protein synthesis rates with a given profile of protein concentrations over time in a circadian system. This protocol can also be applied to a wide range of problems with undetermined dynamics at the upstream levels.

For complete details on the use and execution of this protocol, please refer to Lim et al. (2021).

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Inference of upstream dynamics with information on the downstream profile

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Applies to infer protein synthesis rates with a given circadian protein profile

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Widely applicable to systems biology models with known downstream profiles

A framework of artificial light management for optimal plant development for smart greenhouse application

Smart greenhouse farming has emerged as one of the solutions to global food security, where farming productivity can be managed and improved in an automated manner. While it is known that plant development is highly dependent on the quantity and quality of light exposure, the specific impact of the different light properties is yet to be fully understood. In this study, using the model plant Arabidopsis, we systematically investigate how six different light properties (i.e., photoperiod, light offset, intensity, phase of dawn, duration of twilight and period) would affect plant development i.e., flowering time and hypocotyl (seedling stem) elongation using an established mathematical model of the plant circadian system relating light input to flowering time and hypocotyl elongation outputs for smart greenhouse application. We vary each of the light properties individually and then collectively to understand their effect on plant development. Our analyses show in comparison to the nominal value, the photoperiod of 18 hours, period of 24 hours, no light offset, phase of dawn of 0 hour, duration of twilight of 0.05 hour and a reduced light intensity of 1% are able to improve by at least 30% in days to flower (from 32.52 days to 20.61 days) and hypocotyl length (from 1.90 mm to 1.19mm) with the added benefit of reducing energy consumption by at least 15% (from 4.27 MWh/year to 3.62 MWh/year). These findings could provide beneficial solutions to the smart greenhouse farming industries in terms of achieving enhanced productivity while consuming less energy.