cis Elements and Transcription Factors Regulating Gene Promoters in Response to Environmental Stress
Plants alter their patterns of gene expression in response to environmental stress, and a reprogramming of plant metabolism upon abiotic/biotic stimuli involves changes in plant gene expression. In other words, the expression of many genes involved in pri
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Gene Promoters in Response to Environmental Stress DIETER ERNST and MARK AARTS
6.1 Transcriptional Regulation Plants alter their patterns of gene expression in response to environmental stress, and a reprogramming of plant metabolism upon abiotic/biotic stimuli involves changes in plant gene expression. In other words, the expression of many genes involved in primary and secondary metabolism is induced by various ecotoxicological stressors. Similarly, pathogenesis-related genes are induced by a variety of stressors. These changes are the result of a modification in the rate of transcription for specific genes. An eukaroytic gene is divided into several sections. There is a transcribed region, existing of the coding sequence, a 3' and 5' untranslated region of mRNA, a promoter region and an upstream regulatory region (Ferl and PauI2000). The promoter of a single gene can be activated by different external stimuli, but promoters of different genes can also be activated by the same stimuli. Thus, the organization of different promoter sections and the architecture of promoters contribute to the complex gene regulation upon external stressors. The promoter contains several elements important for the transcription of the protein coding DNA sequence. These regulatory elements are called cis elements. In general these elements are between 4-20 bp long. Not only their sequence is important for controlling transcription, but also their position relative to the transcription start and relative to other cis elements. The basic cis elements of eukaryotic genes are the TATA and CAAT or CCAAT boxes. The TATA box is generally found around 30 bp upstream of the transcription start. Together with the CAAT or CCAAT box, located around 70-80 bp upstream of the transcription start, it is involved in directing the RNA polymerase to the initiation of transcription. In addition to these basic elements, inducible genes contain several other cis elements, which contribute to the final gene regulation upon various abiotic and biotic stimuli, developmental and environmental signal transduction and also tissue specificity (Fig. 6.1) (Hughes 1996; Bray et al. 2000). Analysis of distinct promoter fragments fused to a reporter gene allows the identification of single or Ecological Studies, Vol. 170 H. Sander mann (Ed.) Molecular Ecotoxicology of Plants © Springer-Verlag Berlin Heidelberg 2004
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TF1
cis 2
cis 1
CAAT box
TATA box
Fig.6.1. Promoter organization. The most highly conserved cis element is the TATA box. Several individual cis elements form the basis of a promoter. Transcription factors (TFs) interact with these elements to facilitate transcription
multiple promoter sequence elements that affect the level of gene expression. Substitution mutation analysis of such sequence elements finally results in the identification of DNA motifs for individual cis elements. Technical terms and methods for the identification of cis/trans elements are given in Tables 6.1 and 6.2. Well-known and early characterized cis
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