Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana

BMC Bioinformatics

Research Article

Ban-Dar Hsu¹  Cheng-Wei Yao²  Bor-Sen Chen² 

[1] Department of Life Science, National Tsing Hua University, 300, Hsin-Chu, Taiwan;Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, 300, Hsin-Chu, Taiwan;

关键词: Gene Regulatory Network;    Light Shift;    System Identification Method;    Gene Regulatory System;    Photosystem Stoichiometry;   

DOI  :  10.1186/1471-2105-12-335

 received in 2010-09-22, accepted in 2011-08-11,  发布年份 2011

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Yao et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.