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.
Highlights
Several studies with SR1 have shown that it functions as a negative regulator of plant immunity in Arabidopsis[28,29,30], a positive regulator of insect resistance[31,32] and cold-induced gene expression[24,33]
A very high linear correlation was observed in the expression of genes among the replicates indicating that there are no significant differences in gene expression among the biological replicates (Supplementary Fig. S2)
Expression of about ~85% of differentially expressed (DE) genes was partially or fully restored to wild type level (Supplementary Fig. S3 and Additional File 1, Sheet 2). These results suggest that the DE genes in the mutant are either direct or indirect targets of SR1 and that the loss of this transcription factors (TFs) has substantial effect on expression of large number of genes (Fig. 1A)
Summary
Several studies with SR1 have shown that it functions as a negative regulator of plant immunity in Arabidopsis[28,29,30], a positive regulator of insect resistance[31,32] and cold-induced gene expression[24,33]. SR1 has been shown to play important regulatory roles in plant immunity, herbivory and cold-induced gene expression, the full set of SR1-regulated genes is largely unknown. A previous microarray study performed with wild type and SR1 mutant reported only about 100 SR1-regualted genes[29]. We sequenced the transcriptomes of wild type, SR1 mutant and a complemented line using RNA-seq and identified about 3000 SR1-regulated genes. Comprehensive analysis of SR1-regulated genes confirmed its known roles and uncovered a previously uncharacterized role for SR1 in salt stress. Our results established that SR1 is a negative regulator of salt stress
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