Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice

Mariana Obertello, Stuti Shrivastava, Manpreet S. Katari, Gloria Coruzzi

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1830-1843
Number of pages14
JournalPlant Physiology
Volume168
Issue number4
DOIs
StatePublished - Aug 1 2015

Fingerprint

Arabidopsis
Gene Regulatory Networks
Nitrogen
rice
gene interaction
transcription factors
nitrogen
transcriptome
Transcription Factors
Transcriptome
leucine zipper
hypersensitive response
Biological Phenomena
crops
Leucine Zippers
Genetically Modified Plants
transgenic plants
Oryza sativa
Arabidopsis thaliana
transcription (genetics)

ASJC Scopus subject areas

  • Plant Science
  • Genetics
  • Physiology

Cite this

Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice. / Obertello, Mariana; Shrivastava, Stuti; Katari, Manpreet S.; Coruzzi, Gloria.

In: Plant Physiology, Vol. 168, No. 4, 01.08.2015, p. 1830-1843.

Research output: Contribution to journalArticle

Obertello, Mariana ; Shrivastava, Stuti ; Katari, Manpreet S. ; Coruzzi, Gloria. / Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice. In: Plant Physiology. 2015 ; Vol. 168, No. 4. pp. 1830-1843.
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