Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1

PLoS Genet. 2014 Feb 13;10(2):e1004112. doi: 10.1371/journal.pgen.1004112. eCollection 2014 Feb.

Abstract

Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Cell Death / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genome, Plant
  • Genomics
  • Nuclear Proteins / genetics*
  • Nuclear Proteins / metabolism
  • Reactive Oxygen Species / metabolism*
  • Signal Transduction / genetics*
  • Stress, Physiological / genetics

Substances

  • Arabidopsis Proteins
  • Nuclear Proteins
  • RCD1 protein, Arabidopsis
  • Reactive Oxygen Species

Grants and funding

This work was supported by grants from Biocentrum Helsinki (to JK), the Academy of Finland Center of Excellence in Plant Signal Research (2006–2011), by University of Helsinki (3-year research allocations to MB and KO) and Academy of Finland fellowship and general research grant programs (decision nos. 135751 and 140981 to MB, nos. 251397 and 256073 to KO) and by the Viikki Graduate School in Biosciences (to TB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.