Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi.

Robert C Moseley,Steven B Haase,Francis Motta,Gerald A Tuskan,Xiaohan Yang

doi:10.3390/cells10092217

Robert C Moseley, Steven B Haase + Show 3 more

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https://doi.org/10.3390/cells10092217

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Abstract

The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in Kalanchoë fedtschenkoi. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.

Highlights

The circadian clock is a vital time-keeping mechanism that synchronizes periodic environmental signals to an organism’s physiology, allowing for biological processes to function in a timely manner
The candidate core clock transcription factors (TFs) covered a majority of the phases of the day and displayed a bimodal distribution with peaks occurring before subjective night and before subjective morning (Supplementary Figure S2)
To determine if any of the K. fedtschenkoi TFs were orthologous to A. thaliana TFs that have been annotated as circadian-related, ortholog groups (OGs) constructed in [21] were investigated

Summary

Introduction

The circadian clock is a vital time-keeping mechanism that synchronizes periodic environmental signals to an organism’s physiology, allowing for biological processes to function in a timely manner. This mechanism is very important in plants due to their sessile nature. CAM plants open their stomata during the night allowing for uptake of atmospheric CO2 and close their stomata during the night when normal photosynthetic processes occur [1] This inversion of stomatal movement (i.e., the opening and closing of stomata) is an important drought avoidance/tolerance mechanism in CAM plants, by which water loss caused by evapotranspiration is decreased. The events that lead to these drastic physiological differences seen in CAM plants via the circadian clock are not well understand

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