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

Plant Physiol. 2015 Aug;168(4):1830-43. doi: 10.1104/pp.114.255877. Epub 2015 Jun 4.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Basic-Leucine Zipper Transcription Factors / genetics
  • Basic-Leucine Zipper Transcription Factors / metabolism
  • Gene Expression Profiling*
  • Gene Expression Regulation, Plant / drug effects*
  • Gene Regulatory Networks / drug effects*
  • Models, Genetic
  • Mutation
  • Nitrogen / metabolism
  • Nitrogen / pharmacology*
  • Oryza / genetics*
  • Oryza / metabolism
  • Phylogeny
  • Plant Proteins / classification
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • Plant Shoots / genetics
  • Plant Shoots / metabolism
  • Plants, Genetically Modified
  • Protein Binding
  • Species Specificity
  • Transcription Factors / classification
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Arabidopsis Proteins
  • Basic-Leucine Zipper Transcription Factors
  • HRS1 protein, Arabidopsis
  • Plant Proteins
  • Transcription Factors
  • Nitrogen

Associated data

  • GEO/GSE38102