Regulatory attributes of the carotenoid biosynthetic pathway in Arabidopsis Thaliana under abiotic stress
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Date
2012
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University of the Western Cape
Abstract
Carotenoids are tetraprenoid (C40) molecules synthesized in plants, fungi, bacteria and algae, via the carotenoid biosynthetic pathway (CBP). Some carotenoids are readily converted to vitamin A (VA) in humans, e.g. 13-carotene, c(-carotene and B-cryptoxanthin 1,2. Vitamin a deficiency (VAD) affect millions especially children under the age of five. The CBP in plants is a key source of pro-vitamin A and is vital to the biofortification of staple crops such as maize, rice and sorghum, could alleviate the global VAD problem. However the incomplete understanding of regulation of the pathway is a limiting factor to predictably control carotenoid content at the systems level. Previous studies have shown that growth conditions, such as light, play a major role in the biosynthesis of carotenoids. A systems biology approach was therefore used to analyse microarray data sets derived from A. thaliana grown under various conditions and treated with different stimuli.
Thirty two genes have previously been identified as being involved in the CBP. These genes were found to be highly differentially expressed depending on stress type. All stimuli including drought, cold, heat, osmotic, oxidative and salt but wounding had a significant influence on the CBP genes. Gene expression induced by abiotic stress occured 30 min after exposure. These findings are indicative that an immediate systemic signal is sent to the rest of the plant in response to stress. A correlation analyses revealed strongly positive correlation between PSY and its co-expressed genes, suggesting they share a common regulatory mechanism. Promoter content analyses identified 20 enriched TFBMs among carotenoid genes. The most prevalent TFBMs found in the promoter regions of the CBP genes show a 1.25-3 fold increase in prevalence with a p-value < 0.05. Similar GO terms are enriched for CBP genes and their co-expressed genes. These findings indicate that carotenoid biosynthetic pathway genes and their co-expressed genes are involved in similar metabolic pathways and functional processes. This study identified cold, drought and heat to influence carotenoid gene expression and has led to the identification of molecular switches that can be modulated to control the biosynthetic pathway.
Four motifs without any GO annotation and no specific known motif in plant databases were identified using MEME suite. In this study I propose that these predictions might be novel motifs and could be specific to carotenoid genes, and may be directly involved in the regulation of carotenoid biosynthesis.
These findings may lead to a better understanding of the underlying regulatory mechanisms involved in the biosynthesis of carotenoids. Furthermore, these findings may assist in establishing ways of enhancing the production of carotenoids, especially pro-vitamin A, in Arabidopsis thaliana.
Description
>Magister Scientiae - MSc
Keywords
Vitamin A, Pro- vitamin, Carotenoid biosynthetic pathway, Arabidopsis thaliana, transcription factor binding motif, Promoter, Gene expression, Correlation, Abiotic stress, Microarray, Regulatory networks, Clustering