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Identifying gene regulatory networks common to multiple plant stress responses
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Rhodes, Johanna (2012) Identifying gene regulatory networks common to multiple plant stress responses. PhD thesis, University of Warwick.
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WRAP_THESIS_Rhodes_2012.pdf - Submitted Version Download (5Mb) | Preview |
Official URL: http://webcat.warwick.ac.uk/record=b2680435~S1
Abstract
Stress responses in plants can be defined as a change that affects the homeostasis of pathways,
resulting in a phenotype that may or may not be visible to the human eye, affecting the fitness
of the plant. Crosstalk is believed to be the shared components of pathways of networks, and
is widespread in plants, as shown by examples of crosstalk between transcriptional regulation
pathways, and hormone signalling.
Crosstalk between stress responses is believed to exist, particularly crosstalk within the responses
to biotic stress, and within the responses to abiotic stress. Certain hormone pathways are known
to be involved in the crosstalk between the responses to both biotic and abiotic stresses, and can
confer immunity or tolerance of Arabidopsis thaliana to these stresses. Transcriptional regulation
has also been identified as an important factor in controlling tolerance and resistance to stresses.
In this thesis, networks of regulation mediating the response tomultiple stresses are studied. Firstly,
co-regulation was predicted for genes differentially expressed in two or more stresses by development
of a novel multi-clustering approach, Wigwams Identifies Genes Working Across Multiple
Stresses (Wigwams). This approach finds groups of genes whose expression is correlated within
stresses, but also identifies a strong statistical link between subsets of stresses. Wigwams identifies
the known co-expression of genes encoding enzymes of metabolic and flavonoid biosynthesis
pathways, and predicts novels clusters of co-expressed genes. By hypothesising that by being coexpressed
could also infer that the genes are co-regulated, promoter motif analysis and modelling
provides information for potential upstream regulators.
The context-free regulation of groups of co-expressed genes, or potential regulons, was explored
using models generated by modelling techniques, in order to generate a quantitative model of
transcriptional regulation during the response to B. cinerea, P. syringae pv. tomato DC3000 and
senescence. This model was subsequently validated and extended by experimental techniques,
using Yeast 1-Hybrid to investigate the protein-DNA interactions, and also microarrays. Analysis
of mutants and plants overexpressing a predicted regulator, Rap2.6L, by gene expression analysis
identified a number of potential regulon members as downstream targets.
Rap2.6L was identified as an indirect regulator of the transcription factor members of three potential
regulons co-expressed in the stresses B. cinerea, P. syringae pv. tomato DC3000 and long
day senescence, allowing the confirmation of a predicted gene regulatory network operating in
multiple stress responses.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QK Botany |
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Library of Congress Subject Headings (LCSH): | Gene regulatory networks -- Research, Plants -- Effect of stress on, Plant physiology | ||||
Official Date: | September 2012 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | Systems Biology Doctoral Training Centre | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Denby, Katherine J. | ||||
Extent: | 288 leaves : illustrations, charts | ||||
Language: | eng |
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