Investigation of regulatory elements related to superoxide dismutase enzyme genes in wheat

Introduction: Wheat, like other plants, uses antioxidant enzymes to deal with the high production of free oxygen radicals. Antioxidant enzymes are proteins or polypeptides that are activated in cooperation with cellular substances or mineral elements and are responsible for detoxifying reactive oxygen species in organisms. Superoxide dismutase (SOD) is an important antioxidant enzyme responding to plants' abiotic stresses. This study was performed to identify significant regulatory elements within the promoter regions of superoxide dismutase genes in the wheat genome.
Materials and methods: To investigate the regulation of gene expression and the effective factors in regulating superoxide dismutase enzyme using bioinformatics methods, the promoter region of Mn-SOD, Cu/Zn-SOD and Fe-SOD genes was investigated. The reason for selecting these genes is their ability to scavenge the free radicals of oxygen in plants. Also, their gene expression pattern are crucial under stressful conditions. In order to perform the promotor analysis of these genes, first, the sequence of the genes encoding this enzyme from wheat was downloaded using the NCBI site. After receiving the desired gene sequence, all three sequences of this gene were searched to find different versions of the SOD gene in the wheat genome against the genomic sequence of this plant that has been identified and reported on this site so far. Each received promoter sequence was analyzed and their regulatory elements were identified. Fifteen genes encoding superoxide dismutase were identified and annotated in different chromosomes of A and D genomes of wheat. Then, the promoter regions of these genes, including 1500 bp upstream sequences, were separated to identify the corresponding regulatory elements. The promoter sequences were analyzed to detect the statistically significant over-represented regulatory elements.
Results: The results showed that various regulatory elements involved in different biochemical pathways might influence wheat's transcription of superoxide dismutase genes. G-Box, I-box, MBS, TGA-element, A-box, ABRE, and ARE, are regulatory elements annotated by individual and grouping promoter analysis. In this study, genes encoding superoxide dismutase were mainly identified on different chromosomes of wheat's A and D genomes. This indicates that these genes were probably transferred from the parents of wheat that had these two main genomes to wheat.
Conclusion: Finally, the analysis showed that the important regulatory elements identified in this pathway could include ABRE, ARE, CCAAT-box, G-Box, Skn-1_motif, and circadian, which respectively have a role in the pathway of response to abscisic acid, and response to other reactions such as aerobics reactions, the binding site of elements related to genes encoding MYB transcription factor, response to light conditions, endosperm expression pathway and the pathway of regulation of periodic light responses. Most of the regulatory elements of these genes are involved in light reactions and environmental stresses, which protect the plant against their injury effects.