Analysis of genome-wide targets of Arabidopsis signal responsive 1 (AtSR1) transcription factor and its transcript stability in response to stress
Date
2017
Authors
Abdel-Hameed, Amira, author
Reddy, A. S. N., advisor
Bush, Daniel, committee member
Leach, Jan, committee member
Abdel-Ghany, Salah, committee member
Journal Title
Journal ISSN
Volume Title
Abstract
Abiotic and biotic stresses cause significant yield losses in all crops. Acquisition of stress tolerance in plants requires rapid reprogramming of gene expression. SR1/CAMTA3, a member of signal responsive transcription factors (TFs), functions both as a positive and a negative regulator of biotic stress responses and as a positive regulator of cold stress-induced gene expression. Using high throughput RNA-seq, we identified ~3000 SR1-regulated genes. Promoters of about 60% of the differentially expressed genes have a known DNA binding site for SR1, suggesting that they are likely direct targets. Gene ontology analysis of SR1-regulated genes confirmed previously known functions of SR1 and uncovered a potential role for this TF in salt stress. Our results showed that SR1 mutant is more tolerant to salt stress than the wild type and complemented line. Improved tolerance of sr1 seedlings to salt is accompanied with the induction of salt-responsive genes. Furthermore, ChIP-PCR results showed that SR1 binds to promoters of several salt-responsive genes. These results suggest that SR1 acts as a negative regulator of salt tolerance by directly repressing the expression of salt-responsive genes. Overall, this study identified SR1-regulated genes globally and uncovered a previously uncharacterized role for SR1 in salt stress response. Soil salinity, one of the most prevalent environmental stresses, causes enormous losses in global crop yields every year. Therefore, it is imperative to generate salt tolerant cultivars. To achieve this goal, it is essential to understand the mechanisms by which plants respond to and cope with salt stress. Stress-induced reprogramming of gene expression at multiple levels contributes to the survival of plants under adverse environmental conditions. The control of mRNA stability is one of the post-transcriptional mechanisms that is highly regulated under stress conditions leading to changes in expression pattern of many genes. In this study, we show that salt stress increases the level of SR1 mRNA, by enhancing its stability. Multiple lines of evidence indicate that ROS generated by NADPH oxidase activity mediate salt-induced SR1 transcript stability. Furthermore, cycloheximide (CHX), a protein synthesis inhibitor, also increased SR1 mRNA stability, albeit to a higher level than in the presence of salt, suggesting a role for one or more labile proteins in SR1 mRNA turnover. Similar to salt, ROS generated by NADPH oxidase is also involved in CHX-induced SR1 mRNA accumulation. To gain further insights into mechanisms involved in saltand CHX-induced SR1 stability, the roles of different mRNA degradation pathways were examined in mutants that are impaired in either nonsense-mediated decay (NMD) or mRNA decapping pathways. These studies have revealed that neither the NMD pathway nor the decapping of SR1 mRNA is required for its decay. However, decapping activity is required for saltand CHXaccumulation of SR1 mRNA. To identify any specific regions within the open reading frame of the SR1 transcript (~3 kb) that are responsible for the salt-induced accumulation of SR1 mRNA, we generated transgenic lines expressing several truncated versions of the SR1 coding region in the sr1 mutant background. Then, we analyzed accumulation of each version in response to salt stress and CHX. Interestingly, we identified a 500 nts region in the 3' end of the SR1 coding sequence to be required for both saltand CHX-induced stability of SR1 mRNA. Potential mechanisms by which this region confers SR1 transcript stability in response to salt and CHX are discussed.