Advertisement

3 Biotech

, 8:348 | Cite as

In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

  • Jianbo Song
  • Liming Zeng
  • Rongrong Chen
  • Yihua Wang
  • Yong ZhouEmail author
Original Article

Abstract

Superoxide dismutase (SOD) proteins are crucial antioxidant enzymes that play critical roles in plant growth, development, and response to various abiotic stresses. The SOD gene family has been characterized in various plant species, but not in Medicago truncatula yet. Here, a total of 7 MtSOD genes were first identified from the whole genome of M. truncatula, including 1 MnSOD, 2 FeSODs, and 4 Cu/ZnSODs, which are unevenly distributed in five out of the eight chromosomes. Phylogenetic analysis showed that SOD proteins from M. truncatula and other plant species could be classified into two main categories (Cu/ZnSODs and Fe-MnSODs), which could be further divided into eight subgroups, and members within the same subgroup tended to share the same subcellular localization. In addition, MtSOD genes together with AtSODs and OsSODs within the same subgroup also displayed similar motif compositions and exon–intron structures. Most MtSOD genes were ubiquitously expressed in various tissues, particularly in leaves, seeds and root nodules at different developmental stages. Moreover, microarray analysis and high-throughput sequencing showed that most MtSOD genes were differentially expressed under salt, drought, and cold treatments, indicating their pivotal roles in stress response of M. truncatula. These findings provide useful information for the functional characterization of SOD family genes for growth, development, and stress response of M. truncatula.

Keywords

Medicago truncatula SOD gene family Evolution Expression patterns Abiotic stress 

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31560076 and 31760074).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

13205_2018_1373_MOESM1_ESM.doc (142 kb)
Supplementary material 1 (DOC 141 KB)
13205_2018_1373_MOESM2_ESM.doc (36 kb)
Supplementary material 2 (DOC 35 KB)

References

  1. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208CrossRefPubMedPubMedCentralGoogle Scholar
  2. Corpas FJ, Fernandez-Ocana A, Carreras A, Valderrama R, Luque F, Esteban FJ, Rodriguez-Serrano M, Chaki M, Pedrajas JR, Sandalio LM, del Rio LA, Barroso JB (2006) The expression of different superoxide dismutase forms is cell-type dependent in olive (Olea europaea L.) leaves. Plant Cell Physiol 47:984–994CrossRefPubMedGoogle Scholar
  3. Feng X, Lai Z, Lin Y, Lai G, Lian C (2015) Genome-wide identification and characterization of the superoxide dismutase gene family in Musa acuminata cv. Tianbaojiao (AAA group). BMC Genom 16:823CrossRefGoogle Scholar
  4. Feng K, Yu J, Cheng Y, Ruan M, Wang R, Ye Q, Zhou G, Li Z, Yao Z, Yang Y, Zheng Q, Wan H (2016a) The SOD gene family in tomato: identification, phylogenetic relationships, and expression patterns. Front Plant Sci 7:1279PubMedPubMedCentralGoogle Scholar
  5. Feng X, Chen F, Liu W, Thu MK, Zhang Z, Chen Y, Cheng C, Lin Y, Wang T, Lai Z (2016b) Molecular characterization of MaCCS, a novel copper chaperone gene involved in abiotic and hormonal stress responses in Musa acuminata cv. Tianbaojiao. Int J Mol Sci 17:441CrossRefPubMedPubMedCentralGoogle Scholar
  6. Filiz E, Tombuloğlu H (2015) Genome-wide distribution of superoxide dismutase (SOD) gene families in Sorghum bicolor. Turkish J Biol 39:49–59CrossRefGoogle Scholar
  7. Gill SS, Anjum NA, Gill R, Yadav S, Hasanuzzaman M, Fujita M, Mishra P, Sabat SC, Tuteja N (2015) Superoxide dismutase—mentor of abiotic stress tolerance in crop plants. Environ Sci Pollut Res Int 22:10375–10394CrossRefPubMedGoogle Scholar
  8. Jia Q, Xiao ZX, Wong FL, Sun S, Liang KJ, Lam HM (2017) Genome-wide analyses of the soybean F-box gene family in response to salt stress. Int J Mol Sci 18Google Scholar
  9. Jing X, Hou P, Lu Y, Deng S, Li N, Zhao R, Sun J, Wang Y, Han Y, Lang T, Ding M, Shen X, Chen S (2015) Overexpression of copper/zinc superoxide dismutase from mangrove Kandelia candel in tobacco enhances salinity tolerance by the reduction of reactive oxygen species in chloroplast. Front Plant Sci 6:23CrossRefPubMedPubMedCentralGoogle Scholar
  10. Kaouthar F, Ameny FK, Yosra K, Walid S, Ali G, Faical B (2016) Responses of transgenic Arabidopsis plants and recombinant yeast cells expressing a novel durum wheat manganese superoxide dismutase TdMnSOD to various abiotic stresses. J Plant Physiol 198:56–68CrossRefPubMedGoogle Scholar
  11. Kayum MA, Park JI, Nath UK, Saha G, Biswas MK, Kim HT, Nou IS (2017) Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genom 18:885CrossRefGoogle Scholar
  12. Kliebenstein DJ, Monde RA, Last RL (1998) Superoxide dismutase in Arabidopsis: an eclectic enzyme family with disparate regulation and protein localization. Plant Physiol 118:637–650CrossRefPubMedPubMedCentralGoogle Scholar
  13. Kozik A, Kochetkova E, Michelmore R (2002) GenomePixelizer—a visualization program for comparative genomics within and between species. Bioinformatics 18:335–336CrossRefPubMedGoogle Scholar
  14. Li D, Su Z, Dong J, Wang T (2009) An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genom 10:517CrossRefGoogle Scholar
  15. Li Z, Han X, Song X, Zhang Y, Jiang J, Han Q, Liu M, Qiao G, Zhuo R (2017) Overexpressing the Sedum alfredii Cu/Zn superoxide dismutase increased resistance to oxidative stress in transgenic Arabidopsis. Front Plant Sci 8:1010CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lin YL, Lai ZX (2013) Superoxide dismutase multigene family in longan somatic embryos: a comparison of CuZn-SOD, Fe-SOD, and Mn-SOD gene structure, splicing, phylogeny, and expression. Mol Breed 32:595–615CrossRefGoogle Scholar
  17. Miller AF (2012) Superoxide dismutases: ancient enzymes and new insights. FEBS Lett 586:585–595CrossRefPubMedGoogle Scholar
  18. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plants. Trends Plant Sci 9:490–498CrossRefPubMedGoogle Scholar
  19. Molina-Rueda JJ, Tsai CJ, Kirby EG (2013) The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a). PLoS One 8:e56421CrossRefPubMedPubMedCentralGoogle Scholar
  20. Nath K, Kumar S, Poudyal RS, Yang YN, Timilsina R, Park YS, Nath J, Chauhan PS, Pant B, Lee C-H (2014) Developmental stage-dependent differential gene expression of superoxide dismutase isoenzymes and their localization and physical interaction network in rice (Oryza sativa L.). Genes Genom 36:45–55CrossRefGoogle Scholar
  21. Negi NP, Shrivastava DC, Sharma V, Sarin NB (2015) Overexpression of CuZnSOD from Arachis hypogaea alleviates salinity and drought stress in tobacco. Plant Cell Rep 34:1109–1126CrossRefPubMedGoogle Scholar
  22. Pilon M, Ravet K, Tapken W (2011) The biogenesis and physiological function of chloroplast superoxide dismutases. Biochim Biophys Acta 1807:989–998CrossRefPubMedGoogle Scholar
  23. Song J, Mo X, Yang H, Yue L, Mo B (2017) The U-box family genes in Medicago truncatula: key elements in response to salt, cold, and drought stresses. PLoS One 12:e0182402CrossRefPubMedPubMedCentralGoogle Scholar
  24. 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 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  25. Wang M, Zhao X, Xiao Z, Yin X, Xing T, Xia G (2016a) A wheat superoxide dismutase gene TaSOD2 enhances salt resistance through modulating redox homeostasis by promoting NADPH oxidase activity. Plant Mol Biol 91:115–130CrossRefPubMedGoogle Scholar
  26. Wang W, Xia M, Chen J, Deng F, Yuan R, Zhang X, Shen F (2016b) Genome-wide analysis of superoxide dismutase gene family in Gossypium raimondii and G. arboreum. Plant Gene 6:18–29CrossRefGoogle Scholar
  27. Wang W, Zhang X, Deng F, Yuan R, Shen F (2017) Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. BMC Genom 18:376CrossRefGoogle Scholar
  28. Wu J, Zhang J, Li X, Xu J, Wang L (2016) Identification and characterization of a PutCu/Zn-SOD gene from Puccinellia tenuiflora (Turcz.) Scribn. et Merr. Plant Growth Regul 79:55–64CrossRefGoogle Scholar
  29. Xuan Y, Zhou ZS, Li HB, Yang ZM (2016) Identification of a group of XTHs genes responding to heavy metal mercury, salinity and drought stresses in Medicago truncatula. Ecotoxicol Environ Saf 132:153–163CrossRefPubMedGoogle Scholar
  30. Yan JJ, Zhang L, Wang RQ, Xie B, Li X, Chen RL, Guo LX, Xie BG (2016) The sequence characteristics and expression models reveal superoxide dismutase involved in cold response and fruiting body development in Volvariella volvacea. Int J Mol Sci 17:34–46CrossRefGoogle Scholar
  31. Yang Z, Gong Q, Qin W, Cheng Y, Lu L, Ge X, Zhang C, Wu Z, Li F (2017) Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses. BMC Plant Biol 17:113CrossRefPubMedPubMedCentralGoogle Scholar
  32. Zhang J, Li B, Yang Y, Hu W, Chen F, Xie L, Fan L (2016) Genome-wide characterization and expression profiles of the superoxide dismutase gene family in Gossypium. Int J Genom 2016:8740901Google Scholar
  33. Zhang L, Sun L, Zhang L, Qiu H, Liu C, Wang A, Deng F, Zhu J (2017) A Cu/Zn superoxide dismutase gene from Saussurea involucrata Kar. et Kir., SiCSD, enhances drought, cold and oxidative stress in transgenic tobacco. Can J Plant Sci 97:816–826Google Scholar
  34. Zhou Y, Hu L, Wu H, Jiang L, Liu S (2017) Genome-wide identification and transcriptional expression analysis of cucumber superoxide dismutase (SOD) family in response to various abiotic stresses. Int J Genom 2017:7243973Google Scholar
  35. Zhou Y, Hu L, Ye S, Jiang L, Liu S (2018a) Genome-wide identification of glutathione peroxidase (GPX) gene family and their response to abiotic stress in cucumber. 3 Biotech 8:159CrossRefPubMedGoogle Scholar
  36. Zhou Y, Zeng L, Chen R, Wang Y, Song J (2018b) Genome-wide identification and characterization of the stress associated protein (SAP) gene family encoding A20/AN1 zinc finger proteins in Medicago truncatula. Arch Biol Sci 70:87–98CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Nanchang Economic and Technological Development District, College of ScienceJiangxi Agricultural UniversityNanchangChina
  2. 2.Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of EducationJiangxi Agricultural UniversityNanchangChina

Personalised recommendations