Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana

Abstract

Photosynthesis is one of the most important biological processes on the earth. So far, though the molecular mechanisms underlying photosynthesis is well understood, however, the regulatory networks of photosynthesis are poorly studied. Given the current interest in improving photosynthetic efficiency for greater crop yield, elucidating the detailed regulatory networks controlling the construction and maintenance of photosynthetic machinery is not only scientifically significant but also holding great potential in agricultural application. In this study, we first identified transcription factors (TFs) related to photosynthesis through the TRAP approach using position weight matrix information. Then, for TFs related to photosynthesis, interactions between them and their targets were also determined by the ARACNE approach. Finally, a gene regulatory network was established by combining TF-targets information generated by these two approaches. Topological analysis of the regulatory network suggested that (a) the regulatory network of photosynthesis has a property of “small world”; (b) there is substantial coordination mediated by transcription factors between different components in photosynthesis.

Expression Profiles of <i>psbA, ALS, EPSPS</i>, and Other Chloroplastic Genes in Response to PSII-, ALS-, and EPSPS-Inhibitor Treatments in <i>Kochia scoparia</i>

“…For example, interaction between different components of photosynthetic machinery, as well as with those in pathways associated with amino acid synthesis, stress response, hormonal regulation etc. has been reported [24] [25] [26]. The biochemical pathways that have target sites of most of the commonly used herbicides share a close relation [27].…”

Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis

“…Condition-dependent network analyses can be used to investigate and generate hypotheses related to specific biological processes, for example photosynthesis [4] or nodulation [5]. The gene expression data in these studies are usually produced from a single experiment or retrieved from multiple experiments under a similar set of treatments related to that biological process.…”

Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency

“…Due to the existence of complex regulatory networks that affect photosynthesis (Imam et al ., ; Yu et al ., ) and the large number of genes that are involved, QTL mapping models that solely assume additivity are likely not sufficient to derive a complete comprehension of the genetic architecture of photosynthesis. Epistasis, meaning interaction between genes resulting in non‐additivity of QTLs, has often been regarded as a rather elusive and difficult phenomenon to study, and is therefore often disregarded by plant geneticists and breeders.…”