title: Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana.
abstract: Contextualization of specific transcriptional responses of Arabidopsis within the stress-tissue-time perspective provides a simplified representation of the cellular transcriptional response pathways to abiotic stress, while reducing the dimensions in gene-oriented response description. Crops resistant to abiotic stresses are a long-term goal of many research programs, thus understanding the progression of stress responses is of great interest. We reanalyzed the AtGenExpress transcription dataset to go beyond gene-level characterization, and to contextualize the discrete information into (1) a process-level signature of stress-specific, time-specific, and tissue-specific responses and (2) identify patterns of response progression across a time axis. To gain a functional perspective, ∼1000 pathways associated with the differentially-expressed genes were characterized across all experiments. We find that the global response of pathways to stress is multi-dimensional and does not obviously cluster according to stress, time or tissue. The early response to abiotic stress typically involves induction of genes involved in transcription, hormone synthesis and signaling modules; a later response typically involves metabolism of amino acids and secondary metabolites. By linking specific primary and secondary response pathways, we outline possible stress-associated routes of response progression. The contextualization of specific processes within stress-tissue-time perspective provides a simplified representation of cellular response while reducing the dimensions in gene-oriented response description. Such simplified representation allows finding stress-specific markers based on process-combinations pointing whether a stress-specific response was invoked as well as provide a reference point for the conductance of comparative inter-plant study of stress response, bypassing the need in detailed orthologous mapping.
authors.affiliation: Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Brijesh S
authors.initials: BS
authors.lastname: Yadav
authors.affiliation: Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Lahav
authors.affiliation: Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel.
authors.forename: Eli
authors.initials: E
authors.lastname: Reuveni
authors.affiliation: Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. dannyc@tauex.tau.ac.il.
authors.forename: Daniel A
authors.identifier: http://orcid.org/0000-0002-2815-2909
authors.initials: DA
authors.lastname: Chamovitz
authors.affiliation: Newe-Ya'ar Research Center, Institute of Plant Sciences, Agricultural Research Organization, PO Box 1021, 30095, Ramat Yishay, Israel. shiri@volcani.agri.ac.il.
authors.forename: Shiri
authors.identifier: http://orcid.org/0000-0002-2815-2909
authors.initials: S
authors.lastname: Freilich
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D013312:Stress, Physiological / Q000235:genetics / Q000502:physiology
keywords: Abiotic Stress; Arabidopsis thaliana; Expression data; Metabolic Response; Pathway analysis