Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor

Authors : Ertuğrul FİLİZ, Hüseyin TOMBULOĞLU

Pages : 49-59

Doi:10.3906/biy-1403-9

View : 18 | Download : 8

Publication Date : 2015-12-01

Article Type : Research Paper

Abstract :Superoxide dismutases insert ignore into journalissuearticles values(SODs); are critical enzymes protecting cells against toxic superoxide radicals. To date, 3 types of SODs have been identified: Cu-ZnSODs, Fe-MnSODs, and NiSODs. In this study, a genome-wide analysis was performed in Sorghum bicolor to characterize SOD genes and proteins. Using several bioinformatics tools, we characterized a total of 8 SOD genes from the Sorghum genome. Gene structure, chromosomal distribution, tissue specific expression, conserved domain, and phylogenetic analyses of SOD genes were carried out. Additionally, 3-dimensional structures were determined and compared within each SbSOD protein. Chromosomal distributions revealed that the highest number of SOD genes was on chromosomes 1 and 10, with 2 members on each. Single segmental gene duplication was observed between the genes SbSOD2 and SbSOD5. Intron numbers of SbSOD genes ranged from 5 to 7. Motif analyses showed that SbSODs included 2 and 3 common motifs in Cu-ZnSOD and Fe-MnSODs, respectively. In addition, 3 functional domains were identified in SbSODs: 1); copper-zinc domain insert ignore into journalissuearticles values(Pfam: 00080); in Cu-ZnSOD; and 2); iron/manganese superoxide dismutases alpha-hairpin domain insert ignore into journalissuearticles values(Pfam: 00081); and 3); iron/manganese superoxide dismutases, C-terminal domain insert ignore into journalissuearticles values(Pfam: 02777); in Fe-MnSODs. Gene Ontology term enrichment analysis showed that 8 SOD genes have similar molecular functions and biological processes, and variable cellular components. Phylogenetic analysis revealed that Cu-ZnSODs insert ignore into journalissuearticles values(92%); and Fe-MnSODs insert ignore into journalissuearticles values(100%); were separated by high bootstrap values. Additionally, predicted motif structures and critical binding sites of SbSODs were found to be similar within each SOD group. The results of this study contribute to a better understanding of SOD genes and proteins in plants, especially in Sorghum taxa.
Keywords : Superoxide dismutase, SOD, Sorghum bicolor, genome wide analysis, in silico analysis