Effects of abiotic stress on plants: a systems biology perspective

Abstract

The natural environment for plants is composed of a complex set of abiotic stresses and biotic stresses. Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex networks. Systems biology takes the molecular parts (transcripts, proteins and metabolites) of an organism and attempts to fit them into functional networks or models designed to describe and predict the dynamic activities of that organism in different environments. In this review, research progress in plant responses to abiotic stresses is summarized from the physiological level to the molecular level. New insights obtained from the integration of omics datasets are highlighted. Gaps in our knowledge are identified, providing additional focus areas for crop improvement research in the future.

Figure 1

The number of publications per year related to systems biology and abiotic stress. Key words used in the search of PubMed included: plant, systems biology, and abiotic stress (including stress sub-terms; e.g. drought or water deficit or dehydration). *The number for the year 2011 was estimated by doubling the 6-month value.

Figure 2

A simplified working model of a signaling network of plant responses to abiotic stress. Ovals represent proteins, metabolites or processes. Metabolites have magenta color. Phosphorylated proteins have red circles with a P inside. Sumoylated protein has an orange circle with an S inside. The solid purple circle indicates that DREB2 needs modification to be activated. Solid lines represent direct connections; dotted lines represent indirect connections (acting through some intermediate molecule). The gray line indicates that this reaction has not been shown in plants. Not all linkages and details of stress and hormone effects are shown in this diagram in order to simplify the model. Abbreviations: ABA (abscisic acid), ANAC (Arabidopsis NAC domain-containing protein), CAMTA (calmodulin-binding transcription activator), CBL (calcineurin B-like interacting protein kinase), CCA (circadian clock associated), CPK (calcium-dependent protein kinase), DREB/CBF (dehydration response element binding protein/C-repeat binding factor), ETR1 (ethylene response 1), GCN2 (general control non-repressible 2), HSF (heat shock factor), ICE (inducer of CBF expression), MAPK (mitogen-activated protein kinase), LHY (late elongated hypocotyl), PA (phosphatidic acid), PP2C (protein phosphatase 2C), PRR (pseudo response regulator), PYR/PYL/RCAR (ABA receptors), RNS (reactive nitrogen species), ROS (reactive oxygen species), SIZ (SAP and Miz domain protein), SnRK (sucrose nonfermenting-1 related kinase), TFs (transcription factors), TOR (target of rapamycin), ZAT (zinc finger protein).