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Transcriptome and Proteome Based Survey to Identify Aluminum-Responsive Genes in Roots of Arabidopsis Thaliana Open Access


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Type of item
Degree grantor
University of Alberta
Author or creator
kumari, manjeet
Supervisor and department
Taylor, Gregory (biological sciences)
Deyholos, Mike (biological sciences)
Examining committee member and department
Rahman, Habibur (Agriculture, food, and nutrition sciences)
Good, Allen ( biological sciences)
Gulick, Pat ( Concordia university)
Department of Biological Sciences

Date accepted
Graduation date
Doctor of Philosophy
Degree level
Aluminum (Al)stress is a major limitation to crop productivity on acidic soils. To help understand the cellular mechanisms underlying the toxicity and resistance of plants to Al, this thesis involved a large-scale, transcriptomic and proteomic analysis of roots of Arabidopsis thaliana and reports on comparative analysis of transcriptome and proteome of Al stress responses. Using a microarray representing ~93% of the predicted genes in Arabidopsis, a relatively small proportion (3%) of transcripts were detected as Al- responsive. More changes in the transcriptome were detected after long-term (48 h; 1,114 genes), than short-term (6 h; 401 genes) with relatively little overlap of transcripts detected for each time point. These results suggest that Al toxicity is progressive over time and poses some unique challenges to plants. Further, using two dimensional differential in gel electrophoresis (DiGE), 12 (6 h) and 17 (48 h) proteins were found differentially abundant after Al exposure. Most of the identified proteins were involved in primary metabolism and oxidative stress. Cytosolic-malate dehydrogenase (cyt-MDH) was one of the novel Al-responsive protein identified in this study. Transcript abundance of cyt-MDH correlated well with protein abundance, suggesting that cyt-MDH is regulated in part at transcriptional level. Furthermore, homozygous mdh-1 and mdh-2 mutants were more resistant to Al as compared to WT suggesting that regulation of cyt-MDH could play a role in Al resistance. In general, comparative analysis of proteomics data and transcriptomics data showed a poor correlation for both 6 h (r2 = 0.155) and 48 h (r2 = 0.083). The potential role of five class III peroxidases (PER2, PER27, PER34, PER42, PER69) in resistance of roots to Al was explored using quantitative reverse transcriptase PCR and a reverse genetics approach. A diverse range of patterns of transcript abundance was detected using QRT-PCR in response to Al. Furthermore, per2, per21, and per69 mutants showed greater increases in root lengths as compared to WT after Al stress suggesting that regulation of PER might play a role in Al resistance. These results contribute to the identification of candidate genes for the generation of Al-resistant transgenic plants.
License granted by manjeet kumari ( on 2010-04-15T20:01:28Z (GMT): Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of the above terms. The author reserves all other publication and other rights in association with the copyright in the thesis, and except as herein provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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