Identification of Potato (Solanum tuberosum) SOD Gene Family and Its Response in Damaged Tubers
REN Ying-Yue1, JIANG Hong1, MA Li1, LI Yong-Cai1, Dov Prusky1,2, BI Yang1,*
1 College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, China; 2 Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
Abstract：Superoxide dismutase (SOD) gene family plays an important role in the development and stress response in potato (Solanum tuberosum). However, there are few reports on the identification of SOD gene family members in potato and their gene expression change after tuber damage. In order to analyze the bioinformatics characteristics of potato SOD family members, investigate the expression difference of each family member in different organs of potato seedlings and response in damaged tubers, the softwares GSDS 2.0 and PLACE were used to analyze gene structure and cis-element of StSODs, and the softwares ProtParam, ProtComp 9.0, MEGA7.0, and MEME 4.11.1 were used to analyze physical and chemical properties, subcellular localization, phylogenetic relationship and conserved motifs. The expression level of the gene family numbers was determined in different organs and artificial wounded tuber by qRT-PCR. SOD activity and O2• - and H2O2 contents were analyzed at wounded sites of tubers with 10 mmol/L diethyldithiocarbamate (DDC) treatment by biochemical methods. The results showed that 8 StSODs were identified from the potato genome with different domains such as Cu/ZnSOD domain, Fe/MnSOD α-hairpin domain and C-terminal Fe/MnSOD domain. The amino acid lengths of these StSODs were 152~312 with isoelectric point 5.28~7.13. The predicted subcellular localizations were in the cytoplasm, chloroplast and mitochondria. The StSODs were distributed on 6 of 12 chromosomes unevenly, and divided into 3 subgroups Cu/ZnSOD, FeSOD, and MnSOD, phylogenetically based on their different domains. The promoters of StSODs contained a large number of cis-elements responding to lights, stresses and hormones. StSODs expressed in the roots, stems, leaves, buds and tubers of potato seedling, the expression levels of StCSD1 and StCSD2 in the tuber were significantly higher than that of other organs. The expression of StSODs could be induced at wounded sites of wounded tubers. The expression of StFSD1 and StFSD2 were significantly induced in the early stage, the increased expression of StCSD3 was observed both in early and late stages, while rest SOD genes were expressed in mid stage of the damage. DDC treatment significantly decreased SOD activity and H2O2 content, but increased O2• - content. The present study could provide a reference for further functional study of StSODs in wounded tubers.
[1] 董亮, 何永志, 王远亮, 等.2013.超氧化物歧化酶(SOD)的应用研究进展[J].中国农业科技导报, 15(5): 53-58. (Dong L, He Y Z, Wang Y L, et al.2013.Research progress of superoxide dismutase (SOD)[J].Journal of Agricultural Science and Technology, 15(5): 53-58.) [2] Asao H, Yoshida K, Nishi Y, et al.2003.Wound-responsive cis-element in the 5'-upstream region of cucumber ascorbate oxidase gene[J].Bioscience, Biotechnology, and Biochemistry, 67(2): 271-277. [3] Bradford M M.1976.A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding[J].Analytical Biochemistry, 72(1-2): 248-254. [4] Bernal A, Torres J, Reyes A, et al.2009.Exogenous auxin regulates H2O2 metabolism in roots of tomato (Lycopersicon esculentum mill.) seedlings affecting the expression and activity of CuZn-superoxide dismutase, catalase, and peroxidase[J].Acta Physiologiae Plantarum, 31(2): 249-260. [5] Camp V W, Hérouart D, Willekens H, et al.1996.Tissue-specific activity of two manganese superoxide dismutase promoters in transgenic tobacco[J].Plant Physiology, 112(2): 525-535. [6] Camp V W, Inzé D, Montagu M V.1997.The regulation and function of tobacco superoxide dismutases[J].Free Radical Biology Medicine, 23(3): 515-520. [7] Feng K, Yu J, Cheng Y, et al.2016.The SOD gene family in tomato: Identification, phylogenetic relationships, and expression patterns[J].Frontiers in Plant Science, 7: 1279. [8] Fink R C, Scandalios J G.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[J].Archives of Biochemistry Biophysics, 399(1): 19-36. [9] Fernández-Ocaña A, Chaki M, Luque F, et al.2011.Functional analysis of superoxide dismutases (SODs) in sunflower under biotic and abiotic stress conditions.Identification of two new genes of mitochondrial Mn-SOD[J].Journal of Plant Physiology, 168(11): 1303-1308. [10] Grene A R, Neval E, Heath L S.2002.Role of superoxide dismutases (SODs) in controlling oxidative stress in plants[J].Journal of Experimental Botany, 53(372): 1331-1341. [11] He Z, Zhang H, Gao S, et al.2016.Evolview v2: An online visualization and management tool for customized and annotated phylogenetic trees[J].Nucleic Acids Research, 44(W1): W236-W241. [12] Hu T T, Pattyn P, Bakker E G, et al.2011.The Arabidopsis lyrata genome sequence and the basis of rapid genome size change[J].Nature, 43(5): 476-481. [13] Hérouart D, Marc V M, Inzé D.1994.Developmental and environmental regulation of the Nicotiana plumbaginifolia cytosolic Cu/Zn-superoxide dismutase promoter in transgenic tobacco[J].Plant Physiology, 104(3): 873-880. [14] Heikkila R E, Cabbat F S, Cohen G.1976.In vivo inhibition of superoxide dismutase in mice by diethyldithiocarbamate[J].Journal of Biological Chemistry, 251(7): 2182-2185. [15] Hao F, Zhang J, Yu A, Chen J.2008.Involvement of NADPH oxidase NtrbohD in the rapid production of H2O2 induced by ABA in cultured tobacco cell line BY-2[J].Progress in Natural Science, 18(3): 267-271. [16] Ievinsh G.1992.Soluble lipoxygenase activity in rye seedlings as related to endogenous and exogenous ethylene and wounding[J].Plant Science, 82(2): 155-159. [17] Jacobo-Velázouez D A, González-Agüero M, Cisneros-Zevallos L.2015.Cross-talk between signaling pathways: The link between plant secondary metabolite production and wounding stress response[J].Scientific Reports, 5(1): 8608. [18] Jiang H, Wang B, Ma L, et al.2019.Benzo-(1, 2, 3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) promotes tuber wound healing of potato by elevation of phenylpropanoid metabolism[J].Postharvest Biology and Technology, 153: 125-132. [19] Jasmina K, Hérouart D, Marc V M, et al.1997.Differential expression of CuZn- and Fe-superoxide dismutase genes of tobacco during development, oxidative stress, and hormonal treatments[J].Plant Cell Physiology, 38(4): 463-470. [20] Kolupaev Y E, Firsova E N, Yastreb T O.2017.Induction of plant cells heat resistance by hydrogen sulfide donor is mediated by H2O2 generation with participation of NADPH oxidase and superoxide dismutase[J].The Ukrainian Biochemical Journal, 89(4): 34-42. [21] Lulai E C, Neubauer J D.2014.Wound-induced suberization genes are differentially expressed, spatially and temporally, during closing layer and wound periderm formation[J].Postharvest Biology and Technology, 90(4): 24-33. [22] LI Y, Cao X L, Zhu Y, et al.2019.Osa-miR398b boosts H2O2 production and rice blast disease-resistance via multiple superoxide dismutases[J].New Phytologist, 222(3): 1507-1522. [23] Mahajan N S, Mishra M, Tamhane V A, et al.2014.Stress inducible proteomic changes in Capsicum annuum leaves[J].Plant Physiology Biochemistry, 74: 212-217. [24] Majumdar A, Kumar K R.2018.Orchestration of Cu-Zn SOD and classⅢperoxidase with upstream interplay between NADPH oxidase and PM H+-ATPase mediates root growth in Vigna radiata (L.) Wilczek[J].Journal of Plant Physiology, 232: 248-256. [25] Perl-Treves R, Galun E.1991.The tomato Cu,Zn superoxide dismutase genes are developmentally regulated and respond to light and stress[J].Plant Molecular Biology, 17(4): 745-760. [26] Parker M W, Blake C C F.1988.Iron- and manganese-containing superoxide dismutases can be distinguished by analysis of their primary structures[J].FEBS Letters, 229(2): 377-382. [27] Razem F A, Bemards M A.2003.Reactive oxygen species production in association with suberization: Evidence for an NADPH-dependent oxidase[J].Journal of Experimental Botany, 54(384): 935-941. [28] Rojas-Beltran J A, Dejaeghere F, Kotb M A A, et al.2000.Expression and activity of antioxidant enzymes during potato tuber dormancy[J].Potato Research, 43(4): 383-393. [29] Santos I, Almeida J, Salema R.1999.The influence of UV-B radiation on the superoxide dismutase of maize, potato, sorghum, and wheat leaves[J].Canadian Journal of Botany, 77(1): 70-76. [30] Sudhir K, Glen S, Koichiro T.2016.MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology and Evolution, 33(7): 1870-1874 [31] Schmittgen T D, Livak K J.2008.Analyzing real-time PCR data by the comparative C(T) method[J].Nature Protocols, 3(6): 1101-1108. [32] Sandra K.2002.Tobacco to tomatoes: A phylogenetic perspective on fruit diversity in the Solanaceae[J].Journal of Experimental Botany, 53(377): 2001-2022. [33] Sunkar R, Kapoor A, Zhu J K.2006.Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance[J].Plant Cell, 18(8): 2051-2065. [34] Tamura K, Nei M, Kumar S.2004.Prospects for inferring very large phylogenies by using the neighbor-joining method[J].Proceedings of the National Academy of Sciences of the USA, 101(30): 11030-11035. [35] Tsang E W T, Bowler C, Hérouart D, et al.1991.Differential regulation of superoxide dismutases in plants exposed to environmental stresses[J].Plant Cell, 3(8): 783-792. [36] Wang W, Xia M X, Chen J, et al.2016.Gene expression characteristics and regulation mechanisms of superoxide dismutase and its physiological roles in plants under stress[J].Biochemistry, 81(5): 465-480. [37] Xu X, Pan S K, Cheng S F, et al.2011.Genome sequence and analysis of the tuber crop potato[J].Nature, 475(7355): 189-195. [38] Yadav S, Gill S S, Passricha N, et al.2019.Genome-wide analysis and transcriptional expression pattern-assessment of superoxide dismutase (SOD) in rice and Arabidopsis under abiotic stresses[J].Plant Gene, 17: 100-165.
