From Systems Biology to Gene Function: Discovering New Determinants of Plant Tolerance to Abiotic Stresses

Abstract

Guaranteeing food security in an era of rising world population, global climate change, and pressure to use land situated in harsh environments for agriculture, is an increasing challenge. In the drive for improved crop performance, efforts have focused on identifying genes controlling many traits including greater tolerance to biotic and abiotic stresses. However, several problems in identifying new candidate genes can be distinguished. Classic forward and reverse genetic screens of plant mutants require the screening of up to hundreds of thousands of plants, yet the return is very low -typically <1%-3% of the mutant population display a desired phenotype [1][2][3][4][5][6][7][8]. Although computational methods have shown potential in identifying sets of candidate genes, very few studies have actually tested their predictions on mutant populations. Moreover, most of those studies that have screened mutants defective in candidate genes, have only screened a few mutants, making it difficult to robustly assess gene discovery rate [9][10][11][12][13].We have been employing both systems biology approaches and classic molecular biology techniques, to identify and then characterize useful candidate genes for improving plant stress tolerance. In a recent report, we developed a systems biology-based screen for novel Arabidopsis thaliana abiotic stress regulatory genes that combines gene expression ranking and RNA co-expression analysis, followed by rigorous screening of over 120 T-DNA insertion lines [14,15]. We obtained a remarkable gene discovery rate of 62%, a 48-fold increase over classic genetic screens, and better than any other currently reported computational method. Our co-expression network of Arabidopsis regulatory genes can be inspected at http://netbio.bgu.ac.il/arnet.Mutants of two genes that were identified in our screen exhibited greater tolerance to multiple abiotic stresses as well as enhanced expression of stress-responsive genes, suggesting that the two genes encode negative regulators of Arabidopsis abiotic stress responses [16]. We therefore designated the genes, STRESS RESPONSE SUPPRESSOR (STRS) 1 and STRS 2. Both genes encode members of the DEAD-box RNA helicase family that possess RNA duplex unwinding activity, and can promote duplex formation as well as displacement of proteins from RNA [17]. DEAD-box RNA helicases are involved in virtually all aspects of RNA metabolism, and are often part of supramolecular complexes where they function in remodeling RNA and in assembly of ribonucleoprotein structures. In a recent study, we demonstrated that the STRS proteins are localized to the nucleolus, nucleoplasm and chromocenters (regions of heterochromatic, transcriptionally inactive DNA), and exhibit relocalization in response to abscisic acid (ABA) treatment and various abiotic stresses [18,19]. We also presented strong evidence suggesting that the STRSs are involved in RNA-directed DNA methylation-mediated epigenetic silencing of gene expression to bring about suppression of the Arabidopsis stress re...