Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana

Brijesh S. Yadav; Tamar Lahav; Eli Reuveni; Daniel A. Chamovitz; Shiri Freilich

doi:10.1007/s11103-016-0539-7

Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana

Brijesh S. Yadav, Tamar Lahav, Eli Reuveni, Daniel A. Chamovitz, Shiri Freilich

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Key message: 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. Abstract: 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.

Original language	English
Pages (from-to)	689-699
Number of pages	11
Journal	Plant Molecular Biology
Volume	92
Issue number	6
DOIs	https://doi.org/10.1007/s11103-016-0539-7
State	Published - 1 Dec 2016
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2016, Springer Science+Business Media Dordrecht.

Funding

We thank Profs. Georg Jander, Doron Holland and Gad Galili for helpful comments on the manuscript. We also thank Eyal Zinger and Dr.Â Efrat Oron for technical support related to R and MatLab languages. This research was supported by the I-CORE Program of the Planning and Budgeting Committee, The Israel Science Foundation (Grant No. 757/12) and the Chief Scientist of Israel Ministry of Agriculture and Rural Development (Grant No. 277059016). DAC is a member Edmond J. Safra Center for Bioinformatics at Tel-Aviv University. B.Y.S. was supported by a fellowship from the PBC (Planning and Budgeting Committee) Fellowship Program for Outstanding Post-Doctoral Researchers from India. BSY carried out the analyses and wrote the manuscript; TL aided programming and MatLab analyses; ER aided in gene-enrichment analyses; DAC and SF conceived study, oversaw its execution and wrote the manuscript.

Funders	Funder number
Chief Scientist of Israel Ministry of Agriculture and Rural Development	277059016
Israel Science Foundation	757/12
Israeli Centers for Research Excellence
Planning and Budgeting Committee of the Council for Higher Education of Israel

Keywords

Abiotic Stress
Arabidopsis thaliana
Expression data
Metabolic Response
Pathway analysis

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10.1007/s11103-016-0539-7

Cite this

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abstract = "Key message: 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. Abstract: 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.",

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Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana

Abstract

Bibliographical note

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Keywords

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