Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice

Abstract

In this study, we used a cross-species network approach to uncover nitrogen-regulated network modules conserved across a model and a crop species. By translating gene “network knowledge” from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N-use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated a N-regulatory network based solely on rice (O. sativa) transcriptome and gene interaction data. Next, we enhanced the “network knowledge” in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N-treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to nitrogen use (e.g. N-assimilation) and to other shared biological processes indirectly related to nitrogen. This cross-species network approach was validated with members of two TF families in the supernode network, bZIP-TGA and HRS1/HHO family, have recently been experimentally validated to mediate the N-response in Arabidopsis.