Abstract

BackgroundPhotosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy. However, currently little is known about the molecular mechanisms behind the regulation of the photosynthetic light acclimation response. In this study, a systematic method is proposed to investigate this mechanism by constructing gene regulatory networks from microarray data of Arabidopsis thaliana.MethodsThe potential TF-gene regulatory pairs of photosynthetic light acclimation have been obtained by data mining of literature and databases. Following the identification of these potential TF-gene pairs, they have been refined using Pearson's correlation, allowing the construction of a rough gene regulatory network. This rough gene regulatory network is then pruned using time series microarray data of Arabidopsis thaliana via the maximum likelihood system identification method and Akaike's system order detection method to approach the real gene regulatory network of photosynthetic light acclimation.ResultsBy comparing the gene regulatory networks under the PSI-to-PSII light shift and the PSII-to-PSI light shift, it is possible to identify important transcription factors for the different light shift conditions. Furthermore, the robustness of the gene network, in particular the hubs and weak linkage points, are also discussed under the different light conditions to gain further insight into the mechanisms of photosynthesis.ConclusionsThis study investigates the molecular mechanisms of photosynthetic light acclimation for Arabidopsis thaliana from the physiological level. This has been achieved through the construction of gene regulatory networks from the limited data sources and literature via an efficient computation method. If more experimental data for whole-genome ChIP-chip data and microarray data with multiple sampling points becomes available in the future, the proposed method will be improved on by constructing the whole-genome gene regulatory network. These advances will greatly improve our understanding of the mechanisms of the photosynthetic system.

Highlights

  • Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy

  • We explored The Arabidopsis Information Resource (TAIR) database to obtain annotations of seven TFs in the gene regulatory networks we constructed for this study

  • The photosynthetic light acclimation response is a fundamental process in plants which can optimize the efficiency of photosynthesis in fluctuating light quality

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Summary

Introduction

Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy. The change in redox state of the plastoquinone (PQ) pool of the electron transport chain is the critical regulatory signal source for transcriptional control This change delivers a signal to the nucleus and chloroplast to modulate the expression of photosynthetic genes encoding the PSII and PSI proteins (Figure 1). The primary aim of this study is to use a systems biology approach to investigate the molecular mechanisms of photosynthetic light acclimation by constructing nuclear transcriptional gene regulatory networks under different PQ pool redox states. This has been achieved using time series microarray data of Arabidopsis thaliana under an artificial light system. The artificial light system mimics light conditions by preferentially exciting PSI or PSII to induce more reduced or oxidized states of the PQ pool by shifting from PSI light to PSII light, or from PSII light to PSI light

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