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PMID: 17408486 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.

Genome biology ·Vol. 8 ·No. 4 ·2007-00-00 ·Pages R49

Ma S, Bohnert HJ

Abstract

Arabidopsis thaliana transcript profiles indicate effects of abiotic and biotic stresses and tissue-specific and cell-specific gene expression. Organizing these datasets could reveal the structure and mechanisms of responses and crosstalk between pathways, and in which cells the plants perceive, signal, respond to, and integrate environmental inputs. We clustered Arabidopsis transcript profiles for various treatments, including abiotic, biotic, and chemical stresses. Ubiquitous stress responses in Arabidopsis, similar to those of fungi and animals, employ genes in pathways related to mitogen-activated protein kinases, Snf1-related kinases, vesicle transport, mitochondrial functions, and the transcription machinery. Induced responses to stresses are attributed to genes whose promoters are characterized by a small number of regulatory motifs, although secondary motifs were also apparent. Most genes that are downregulated by stresses exhibited distinct tissue-specific expression patterns and appear to be under developmental regulation. The abscisic acid-dependent transcriptome is delineated in the cluster structure, whereas functions that are dependent on reactive oxygen species are widely distributed, indicating that evolutionary pressures confer distinct responses to different stresses in time and space. Cell lineages in roots express stress-responsive genes at different levels. Intersections of stress-responsive and cell-specific profiles identified cell lineages affected by abiotic stress. By analyzing the stress-dependent expression profile, we define a common stress transcriptome that apparently represents universal cell-level stress responses. Combining stress-dependent and tissue-specific and cell-specific expression profiles, and Arabidopsis 5'-regulatory DNA sequences, we confirm known stress-related 5' cis-elements on a genome-wide scale, identify secondary motifs, and place the stress response within the context of tissues and cell lineages in the Arabidopsis root.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Cell Lineage Cluster Analysis Databases, Genetic Gene Expression Profiling Gene Expression Regulation, Plant Homeostasis/genetics Models, Genetic Oligonucleotide Array Sequence Analysis Plant Roots/genetics,metabolism Promoter Regions, Genetic RNA, Messenger/metabolism Regulatory Elements, Transcriptional Signal Transduction/genetics
Chemicals
Arabidopsis Proteins RNA, Messenger
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ma Shisong
Physiological and Molecular Plant Biology Graduate Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. [email protected]
Bohnert Hans J
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2007-8-4-r49
Email
[email protected]
Published
2007-00-00
Pages
R49
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1896000
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2007-8-4-r49 PMC Full Text View journal details
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