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

Superoxide dismutases (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 (Pfam: 00080) in Cu-ZnSOD; and 2) iron/manganese superoxide dismutases alpha-hairpin domain (Pfam: 00081) and 3) iron/manganese superoxide dismutases, C-terminal domain (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 (92%) and Fe-MnSODs (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.

Anahtar Kelimeler:

Superoxide dismutase, SOD, Sorghum bicolor, genome-wide analysis, in silico analysis

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

Keywords:

Superoxide dismutase, SOD, Sorghum bicolor, genome-wide analysis, in silico analysis,

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Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al. (2000). Gene Ontology: tool for the unification of biology. Nat Genet 25: 25–29.
Bailey TL, Boden M, Buske FA, Frith M, Grant C, Clementi L, Ren J, Li WW, Noble WS (2009). MEME SUITE: tools for motif discovery and searching. Nucl Acids Res 37: 202–208.
Bhattacharjee S (2012). The language of reactive oxygen species signaling in plants. Journal of Botany 2012: 985298.
Bueno P, Varela J, Giménez-Gallego G, Del Río LA (1995). Peroxisomal copper, zinc superoxide dismutase-characterization of the isoenzyme from watermelon cotyledons. Plant Physiol 108: 1151–1160.
Carlioz A, Touati D (1986). Isolation of superoxide dismutase mutants in Escherichia coli: is superoxide dismutase necessary for aerobic life? EMBO J 5: 623–630.
Dehury B, Sarma K, Sarmah R, Sahu J, Sahoo S, Sahu M, Sen P, Modi KM, Barooah M (2012). In silico analyses of superoxide dismutases (SODs) of rice (Oryza sativa L.). J Plant Biochem Biotechnol 22: 150–156.
Filiz E, Koç I, Tombuloğlu H (2014). Genome-wide identification and analysis of growth regulating factor genes in Brachypodium distachyon: in silico approaches. Turk J Biol 38: 296–306.
Fink RC, Scandalios JG (2002). Molecular evolution and structure- function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases. Arch Biochem Biophys 399: 19–36.
Ganko EW, Meyers BC, Vision TJ (2007). Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 24: 2298–2309.
Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH (2002). Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19: 256–262.
Guo AY, Zhu QH, Chen X, Luo JC (2007). GSDS: a gene structure display server. Yi Chuan 29: 1023–1026.
Higgins DG, Thompson JD, Gibson TJ (1996). Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266: 383– 402.
Kliebenstein DJ, Monde RA, Last RL (1998). Superoxide dismutase in Arabidopsis: an eclectic enzyme family with disparate regulation and protein localization. Plant Physiol 118: 637–650.
Lawton-Rauh A (2003). Evolutionary dynamics of duplicated genes in plants. Mol Phylogenet Evol 29: 396–409.
Lazarides M, Hacker JB, Andrew MH (1991). Taxonomy, cytology and ecology of indigenous Australian sorghums (Sorghum Moench: Andropogoneae: Poaceae). Aust Syst Bot 4: 591–635.
Lovell SC, Davis IW, Bryan Arendall W, Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003). Structure validation by Cα geometry: φ, ψ, and Cβ deviation. Proteins 50: 437–450.
Miller AF (2012). Superoxide dismutases: ancient enzymes and new insights. FEBS Lett 586: 585–595.
Miller G, Shulaev V, Mittler R (2008). Reactive oxygen signaling and abiotic stress. Physiol Plantarum 133: 481–489.
Mittler R, Blumwald E (2010). Genetic engineering form modern agriculture: challenges and perspectives. Annu Rev Plant Biol 61: 443–462.
Mittler R, Vanderauwera S, Gollery M, Breusegem FN (2004). Reactive oxygen gene network of plants. Trends Plant Sci 9: 490–498.
Mİller IM (2001). Plant mitochondria and oxidative stress: electron transport, NADPH turnover, and metabolism of reactive oxygen species. Annu Rev Plant Physiol Plant Mol Biol 52: 561–91.
Moran JF, James EK, Rubio MC, Sarath G, Klucas RV, Becana M (2003). Functional characterization and expression of a cytosolic iron superoxide dismutase from cowpeak root nodules. Plant Physiol 133: 773–782.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556.
Perry JJP, Shin DS, Getzoff ED, Tainer JA (2010). The structural biochemistry of the superoxide dismutases. Biochim Biophys Acta 1804: 245–262.
Price HJ, Dillon SN, Hodnett G, Rooney WL, Ross L, Johnston JS (2005). Genome evolution in the genus Sorghum (Poaceae). Ann Bot 95: 219–227.
Qu CP, Xu ZR, Liu GJ, Liu C, Li Y, Wei ZG, Liu GF (2010). Differential expression of copper-zinc superoxide dismutase gene of Polygonum sibiricum leaves, stems, and underground stems, subjected to high-salt stress. Int J Mol Sci 11: 5234–5245.
Sharma P, Jha AB, Dubey RS, Pessarakli M (2012). Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. Journal of Botany 2012: 217037.
Sonnhammer EL, Eddy SR, Durbin R (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28: 405–420.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
Wass MN, Kelley LA, Sternberg MJ (2010). 3DLigandSite: predicting ligand-binding sites using similar structures. Nucl Acid Res 38 (Suppl.): W469–473.
Wolfe-Simon F, Schofield DGO, Falkowski PG (2005). The role and evolution of superoxide dismutase in algae. J Phycol 41: 453– 465.
Xu G, Guo C, Shan H, Kong H (2012). Divergence of duplicate genes in exon–intron structure. P Natl Acad Sci USA 109: 1187–1192.
Yang S, Zhang X, Yue JX, Tian D, Chen JQ (2008). Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics 280: 187–198.
Youn HD, EJ Kim, JH Roe, YC Hah, SO Kang (1996). A novel nickel- containing superoxide dismutase from Streptomyces spp. Biochem J 318: 889–896.