Genome-wide identification and gene expression analysis of SOS family genes in tuber mustard (Brassica juncea var. tumida)

Autoři: Chunhong Cheng aff001;  Yuanmei Zhong aff001;  Qing Wang aff001;  Zhaoming Cai aff001;  Diandong Wang aff001;  Changman Li aff001
Působiště autorů: School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, P.R. China aff001
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
prolekare.web.journal.doi_sk: 10.1371/journal.pone.0224672


The Salt Overly Sensitive (SOS) pathway in Arabidopsis thaliana plays important roles in maintaining appropriate ion homeostasis in the cytoplasm and regulating plant tolerance to salinity. However, little is known about the details regarding SOS family genes in the tuber mustard crop (Brassica juncea var. tumida). Here, 12 BjSOS family genes were identified in the B. juncea var. tumida genome including two homologous genes of SOS1, one and three homologs of SOS2 and SOS3, two homologs of SOS4, two homologs of SOS5 and two homologs of SOS6, respectively. The results of conserved motif analysis showed that these SOS homologs contained similar protein structures. By analyzing the cis-elements in the promoters of those BjSOS genes, several hormone- and stress-related cis-elements were found. The results of gene expression analysis showed that the homologous genes were induced by abiotic stress and pathogen. These findings indicate that BjSOS genes play crucial roles in the plant response to biotic and abiotic stresses. This study provides valuable information for further investigations of BjSOS genes in tuber mustard.

Klíčová slova:

Gene expression – Sequence alignment – Gene regulation – Sequence motif analysis – Plant resistance to abiotic stress – Protein structure comparison – Arabidopsis thaliana – Tubers


1. Yang J, Liu D, Wang X, Ji C, Cheng F, Liu B, et al. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat. Genet. 2016, 48, 1225–1232. doi: 10.1038/ng.3657 27595476

2. Shi HZ, Ishitani M, Kim CS, Zhu JK. The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. Proc. Natl. Acad. Sci. USA. 2000, 97, 6896–6901. doi: 10.1073/pnas.120170197 10823923

3. Liu J, Ishitani M, Halfter U, Kim CS, Zhu JK. The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proc. Natl. Acad. Sci. USA. 2000, 97, 3730–3734. doi: 10.1073/pnas.060034197 10725382

4. Gong D, Guo Y, Schumaker KS, Zhu JK. The SOS3 family of calcium sensors and SOS2 family of protein kinases in Arabidopsis. Plant Physiol. 2004, 134, 919–926. doi: 10.1104/pp.103.037440 15020756

5. Qiu QS, Guo Y, Dietrich MA, Schumaker KS, Zhu JK. Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3. Proc. Natl. Acad. Sci. USA. 2002, 99, 8436–8441. doi: 10.1073/pnas.122224699 12034882

6. Zhu JK. Regulation of ion homeostasis under salt stress. Curr. Opin. Plant Biol. 2003, 6, 441–445. 12972044

7. Shi H, Xiong L, Stevenson B, Lu T, Zhu JK. The Arabidopsis salt overly sensitive 4 Mutants Uncover a Critical Role for Vitamin B6 in Plant Salt Tolerance. Plant Cell. 2002, 14, 575–588. doi: 10.1105/tpc.010417 11910005

8. Shi H, Zhu JK. SOS4, A Pyridoxal Kinase Gene, Is Required for Root Hair Development in Arabidopsis. Plant Physiol. 2002, 129, 585–593. doi: 10.1104/pp.001982 12068103

9. Shi H, Kim Y, Guo Y, Stevenson B, Zhu JK. The Arabidopsis SOS5 Locus Encodes a Putative Cell Surface Adhesion Protein and Is Required for Normal Cell Expansion. Plant cell. 2003, 15, 19–32. doi: 10.1105/tpc.007872 12509519

10. Zhu JH, Lee BH, Dellinger M, Cui XP, Zhang CQ, Wu S, et al. A cellulose synthase‐like protein is required for osmotic stress tolerance in Arabidopsis. The Plant Journal. 2010, 63, 128–140. doi: 10.1111/j.1365-313X.2010.04227.x 20409003

11. Zhu JK, Liu J, Xiong L. Genetic analysis of salt tolerance in Arabidopsis evidence for a critical role of potassium nutrition. Plant Cell. 1998, 10, 1181–1191. doi: 10.1105/tpc.10.7.1181 9668136

12. Shi H, Lee BH, Wu SJ, Zhu JK. Overexpression of a plasmamembrane Na+/H+ antiporter gene improves salt tolerance in Arabidopsis thaliana. Nat. Biotechnol. 2003, 21, 81–85. doi: 10.1038/nbt766 12469134

13. Nutan KK, Kumar G, Singla-Pareek SL, Pareek A. A salt overly sensitive pathway member from Brassica juncea BjSOS3 can functionally complement ΔAtsos3 in Arabidopsis. Curr. Genomics. 2017, 19, 60–69.

14. Kumar G, Purty RS, Sharma MP, Singla-Pareek SL, Pareek A. Physiological response among Brassica species under salinity stress show strong correlation with transcript abundance for SOS pathway-related genes. Plant Physiol. 2009, 166, 507–520.

15. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876–4882. doi: 10.1093/nar/25.24.4876 9396791

16. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28, 2731–2739. doi: 10.1093/molbev/msr121 21546353

17. Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M, et al. Transcriptional regulation of ABI3- and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis. Plant Mol. Biol. 2006, 60, 51–68. doi: 10.1007/s11103-005-2418-5 16463099

18. Mena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P. A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiol. 2002, 130, 111–119. doi: 10.1104/pp.005561 12226491

19. Despres C, Chubak C, Rochon A, Clark R, Bethune T, Desveaux D, et al. The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell. 2003, 15, 2181–2191. doi: 10.1105/tpc.012849 12953119

20. Baker SS, Wilhelm KS, Thomashow MF. The 5'-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol. Biol. 1994, 24, 701–713. doi: 10.1007/bf00029852 8193295

21. Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell 1993, 5, 1529–1539. doi: 10.1105/tpc.5.11.1529 8312738

22. Chakravarthy S, Tuori RP, DAscenzo MD, Fobert PR, Despres C, Martin GB. The tomato transcription factor Pti4 regulates defence-related gene expression via GCC box and non-GCC box cis elements. Plant Cell 2003, 15, 3033–3050. doi: 10.1105/tpc.017574 14630974

23. Dunn MA, White AJ, Vural S, Hughes MA. Identification of promoter elements in a low-temperature-responsive gene (blt4.9) from barley (Hordeum vulgare L.). Plant Mol. Biol. 1998, 38, 551–564. doi: 10.1023/a:1006098132352 9747801

24. Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, et al. Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant Physiol. 2004, 135, 2150–2161. doi: 10.1104/pp.104.041442 15310827

25. Chen J, Piao Y, Liu Y, Li X, Piao Z. Genome-wide identification and expression analysis of chitinase gene family in, Brassica rapa, reveals its role in clubroot resistance. Plant Sci. 2018, 270, 257–267. doi: 10.1016/j.plantsci.2018.02.017 29576079

26. Goyal E, Singh RS, Kanika K. Isolation and functional characterization of Salt overly sensitive 1 (SOS1) gene promoter from Salicornia brachiata. Biol. Plantarum. 2013, 57, 465–473.

27. Kaur C, Kumar G, Kaur S, Ansari MW, Pareek A, Sopory SK, et al. Molecular cloning and characterization of salt overly sensitive gene promoter from Brassica juncea (BjSOS2). Mol. Biol. Rep. 2015, 42, 1139–1148. doi: 10.1007/s11033-015-3851-4 25633281

28. Feki K, Brini F, Amar SB, Saibi W, Masmoudi K. Comparative functional analysis of two wheat Na+/H+ antiporter SOS1 promoters in Arabidopsis thaliana under various stress conditions. J. Appl. Genet. 2015, 56, 15–26. doi: 10.1007/s13353-014-0228-7 25081835

29. Sathee L, Sairam RK, Chinnusamy V, et al. Differential transcript abundance of salt overly sensitive (SOS) pathway genes is a determinant of salinity stress tolerance of wheat. Acta Physiol. Plant. 2015, 37, 169.

30. Chakraborty K, Sairam RK, Bhattacharya RC. Differential expression of salt overly sensitive pathway genes determines salinity stress tolerance in Brassica genotypes. Plant Physiol. Biochem. 2012, 51, 90–101. doi: 10.1016/j.plaphy.2011.10.001 22153244

31. Shi H, Quintero FJ, Pardo JM, Zhu JK. The putative plasma membrane Na(+)/H(+) antiporter SOS1 controls long-distance Na(+) transport in plants. The Plant Cell. 2002, 14, 465–477. doi: 10.1105/tpc.010371 11884687

32. Martínez-Atienza J, Jiang X, Garciadeblas B, Mendoza I, Zhu JK, Pardo JM, et al. Conservation of the salt overly sensitive pathway in rice. Plant Physiol. 2007, 143, 1001–1012. doi: 10.1104/pp.106.092635 17142477

33. Tang RJ, Liu H, Bao Y, Lv QD, Yang L, Zhang HX. The woody plant poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress. Plant Mol. Biol. 2010, 74, 367–380. doi: 10.1007/s11103-010-9680-x 20803312

34. Di F, Jian H, Wang T, Chen X, Ding Y, Du H, et al. Genome-wide analysis of the PYL gene family and identification of PYL genes that respond to abiotic stress in Brassica napus. Genes. 2018, 9, 156.

35. Cai Z, Zeng DE, Liao J, Cheng C, Sahito ZA, Xiang M, et al. Genome-wide analysis of auxin receptor family genes in Brassica juncea var. tumida. Genes. 2019, 10, 165.

Článok vyšiel v časopise


2019 Číslo 11