Effects of abiotic stress on plants: a systems biology perspective

Recent advances in biotechnology have dramatically changed our capabilities for gene discovery and functional genomics. For the first time, we can now obtain a holistic "snapshot" of a cell with transcript, protein and metabolite profiling. Such a "systems biology" approach allows for a deeper understanding of physiologically complex processes and cellular function [1]. New models can be formed from the plethora of data collected and lead to new hypotheses generated from those models.Understanding the function of genes is a major challenge of the post-genomic era. While many of the functions of individual parts are unknown, their function can sometimes be inferred through association with other known parts, providing a better understanding of the biological system as a whole. High throughput omics technologies are facilitating the identification of new genes and gene function. In addition, network reconstructions at the genome-scale are key to quantifying and characterizing the genotype to phenotype relationships [2].In this review, we summarize recent progress on systematic analyses of plant responses to abiotic stress to include transcriptomics, metabolomics, proteomics, and other integrated approaches. Due to space limitations, we try to emphasize important perspectives, especially from what systems biology and omics approaches have provided in recent research on environmental stresses.Plants are complex organisms. It is difficult to find an estimate of the total number of cells in a plant. Estimates of the number of cells in the adaxial epidermal layer and palisade mesophyll of a simple Arabidopsis leaf are approximately 27,000 and 57,000 cells, respectively [3]. Another estimate of the adaxial side of the epidermal layer of the 7th leaf of Arabidopsis was close to 100,000 cells [4] per cm2 of leaf area. An Arabidopsis plant can grow as large as 14 g fresh weight with a leaf area of 258 cm2 (11 g fresh weight) [5]. Thus, we estimate that a single Arabidopsis pla