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 (N)-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, rice (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 an N-regulatory network based solely on rice 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 N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis.

Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks

“…Remarkably, the universal nitrate-inducible genes responsible for the conserved nitrogen uptake and assimilation processes from Arabidopsis , rice to maize were regulated by CPK10/30/32 (Extended Data Fig. 4e-g) 1,3,4,12,17,18,21,32 . Nearly 50 genes encoding annotated TFs were activated by nitrate via CPK10/30/32 (Supplementary Table 2), providing potential amplification of the downstream nitrate transcriptional network 17,18,20,24,25 .…”

“…Error bars, s.d., n=3 biological replicates. NITRATE REDUCTASE1/2 ( NIA1/2), NIR, NITRATE TRANSPORTER2.1/2.2 (NRT2.1/2.2), G6PD2/3, GLUTAMINE SYNTHETASE (GLN), GLUTAMATE DEHYDROGENASE3 (GDH3), UROPORPHYRINOGEN III METHYLTRANSFERASE1 (UPM1), FERREDOXIN3 (FD3) and FNR1/2 , were regulated by CPK10/30/32 1,3,4,12,17,18,21,32 . TF genes, NLP3, HRS1 ( HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 ) and TGA4 (TGACG MOTIF-BINDING FACTOR 4) were primary nitrate-CPK target genes 12,17,18,20,24 .…”

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

“…For rice, where only a minority of regulatory relationships are known, several EGRINs have been published that use additional knowledge of network regulators to inform transcriptomebased network inference models. For example, Obertello et al (2015) included knowledge of regulatory interactions in other species, and Nigam et al (2015) consider microRNA-mediated TF activity. In both of these instances, the additional data types were used to filter and refine coexpression networks.…”

Environmental gene regulatory influence networks in rice (Oryza sativa):response to water deficit, high temperature and agricultural environments

“…For rice, where only a minority of regulatory relationships are known, several EGRINs have been published that use additional knowledge of network regulators to inform transcriptome-based network inference models. For example, Obertello et al, (2015) included knowledge of regulatory interactions in other species, and Nigam et al, (Nigam et al, 2015) consider microRNAmediated TF activity. In both of these instances, the additional data types were used to filter and refine co-expression networks.…”