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Characterizing the stress/defense transcriptome of Arabidopsis.

Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R, Fedoroff NV - Genome Biol. (2003)

Bottom Line: Several stress-responsive cis-elements showed a statistically significant over-representation in the promoters of the genes in the stress cDNA collection.These include W- and G-boxes, the SA-inducible element, the abscisic acid response element and the TGA motif.This set of stress-, pathogen- and hormone-modulated genes is an important resource for understanding the genetic interactions underlying stress signaling and responses and may contribute to the characterization of the stress transcriptome through the construction of standardized specialized arrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Consortium, Pennsylvania State University, State College, PA 16802, USA.

ABSTRACT

Background: To understand the gene networks that underlie plant stress and defense responses, it is necessary to identify and characterize the genes that respond both initially and as the physiological response to the stress or pathogen develops. We used PCR-based suppression subtractive hybridization to identify Arabidopsis genes that are differentially expressed in response to ozone, bacterial and oomycete pathogens and the signaling molecules salicylic acid (SA) and jasmonic acid.

Results: We identified a total of 1,058 differentially expressed genes from eight stress cDNA libraries. Digital northern analysis revealed that 55% of the stress-inducible genes are rarely transcribed in unstressed plants and 17% of them were not previously represented in Arabidopsis expressed sequence tag databases. More than two-thirds of the genes in the stress cDNA collection have not been identified in previous studies as stress/defense response genes. Several stress-responsive cis-elements showed a statistically significant over-representation in the promoters of the genes in the stress cDNA collection. These include W- and G-boxes, the SA-inducible element, the abscisic acid response element and the TGA motif.

Conclusions: The stress cDNA collection comprises a broad repertoire of stress-responsive genes encoding proteins that are involved in both the initial and subsequent stages of the physiological response to abiotic stress and pathogens. This set of stress-, pathogen- and hormone-modulated genes is an important resource for understanding the genetic interactions underlying stress signaling and responses and may contribute to the characterization of the stress transcriptome through the construction of standardized specialized arrays.

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A pie chart showing the fraction of stress-modulated genes in each of the functional categories described in Bevan et al. [38].
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Figure 5: A pie chart showing the fraction of stress-modulated genes in each of the functional categories described in Bevan et al. [38].

Mentions: With the information gathered from the MIPS Arabidopsis database [36] and InterPro protein domain searches [37] we were able to identify or assign putative functions to about three-quarters (764) of the genes in the stress cDNA collection. More than 290 SSH clones encoded proteins with insufficient similarity to proteins of known function to assign a function with confidence, and we therefore classified them as being of unknown function. The genes of known function were sorted into the 12 primary functional categories [38]. The distribution of the genes with known or predicted functions is represented as a pie chart in Figure 5. The largest set of genes (15%) was assigned to the metabolism category, while genes involved in cell growth/division constituted the smallest group, comprising less than 2% of the genes. Genes involved in signal transduction and protein destination/storage formed the second (13%) and third largest groups (12%), respectively. Genes implicated in stress/defense response and genes involved in transcription together constituted 20% of the stress cDNA collection (Figure 5).


Characterizing the stress/defense transcriptome of Arabidopsis.

Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R, Fedoroff NV - Genome Biol. (2003)

A pie chart showing the fraction of stress-modulated genes in each of the functional categories described in Bevan et al. [38].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC153460&req=5

Figure 5: A pie chart showing the fraction of stress-modulated genes in each of the functional categories described in Bevan et al. [38].
Mentions: With the information gathered from the MIPS Arabidopsis database [36] and InterPro protein domain searches [37] we were able to identify or assign putative functions to about three-quarters (764) of the genes in the stress cDNA collection. More than 290 SSH clones encoded proteins with insufficient similarity to proteins of known function to assign a function with confidence, and we therefore classified them as being of unknown function. The genes of known function were sorted into the 12 primary functional categories [38]. The distribution of the genes with known or predicted functions is represented as a pie chart in Figure 5. The largest set of genes (15%) was assigned to the metabolism category, while genes involved in cell growth/division constituted the smallest group, comprising less than 2% of the genes. Genes involved in signal transduction and protein destination/storage formed the second (13%) and third largest groups (12%), respectively. Genes implicated in stress/defense response and genes involved in transcription together constituted 20% of the stress cDNA collection (Figure 5).

Bottom Line: Several stress-responsive cis-elements showed a statistically significant over-representation in the promoters of the genes in the stress cDNA collection.These include W- and G-boxes, the SA-inducible element, the abscisic acid response element and the TGA motif.This set of stress-, pathogen- and hormone-modulated genes is an important resource for understanding the genetic interactions underlying stress signaling and responses and may contribute to the characterization of the stress transcriptome through the construction of standardized specialized arrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Consortium, Pennsylvania State University, State College, PA 16802, USA.

ABSTRACT

Background: To understand the gene networks that underlie plant stress and defense responses, it is necessary to identify and characterize the genes that respond both initially and as the physiological response to the stress or pathogen develops. We used PCR-based suppression subtractive hybridization to identify Arabidopsis genes that are differentially expressed in response to ozone, bacterial and oomycete pathogens and the signaling molecules salicylic acid (SA) and jasmonic acid.

Results: We identified a total of 1,058 differentially expressed genes from eight stress cDNA libraries. Digital northern analysis revealed that 55% of the stress-inducible genes are rarely transcribed in unstressed plants and 17% of them were not previously represented in Arabidopsis expressed sequence tag databases. More than two-thirds of the genes in the stress cDNA collection have not been identified in previous studies as stress/defense response genes. Several stress-responsive cis-elements showed a statistically significant over-representation in the promoters of the genes in the stress cDNA collection. These include W- and G-boxes, the SA-inducible element, the abscisic acid response element and the TGA motif.

Conclusions: The stress cDNA collection comprises a broad repertoire of stress-responsive genes encoding proteins that are involved in both the initial and subsequent stages of the physiological response to abiotic stress and pathogens. This set of stress-, pathogen- and hormone-modulated genes is an important resource for understanding the genetic interactions underlying stress signaling and responses and may contribute to the characterization of the stress transcriptome through the construction of standardized specialized arrays.

Show MeSH
Related in: MedlinePlus