Comparative Analysis of Sequence, Chromosomal Arrangement and Cis-Regulatory Elements of SQS Genes Across Brassicaceae
DOI:
https://doi.org/10.55863/ijees.2024.0316Keywords:
Brassicaceae, Cis-regulatory elements, Evolutionary analysis, Gene duplication, Phytosterols, Squalene synthase (SQS)Abstract
Plant sterols are known to be involved in plant growth and development and also in plants' response to stress conditions. Squalene synthase (SQS) is an important enzyme for the biosynthesis of sterols and triterpenoids. Owing to their crucial role in plants, SQS genes have been identified and characterized in several plants, however not much is known about their cis-regulatory regions. In our previous study, we identified Brassicaceae specific duplications of the gene, providing an ideal opportunity to explore the diversification of the regulatory regions across the gene copies. In this study we identified 49 SQS genes from 12 species of Brassicaceae and analyzed their genomic distribution, physicochemical properties, subcellular localization, cis-regulatory element (CRE) landscape and sequence evolution (Ka/Ks ratios). The SQS proteins were predicted to be highly stable, dominated by aliphatic amino acids, hydrophilic in nature and localized within the endoplasmic reticulum. In-silico promoter analysis identified 50 types of CREs with the predominance of light-responsive (22), followed by hormone-responsive (9), stress-responsive (7) and plant growth and development (9) elements. We identified differences both in the type and distribution of CREs across the SQS duplicates suggestive of regulatory divergence of the paralogs. The Ka/Ks analysis depicted that all the SQS genes are under purifying selection pressure. The information generated in this study would provide a useful resource for further investigations in SQS genes in Brassicaceae.
References
Arsovski, A.A., Pradinuk, J., Guo, X.Q., Wang, S. and Adams, K.L. 2015. Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis. Plant physiology, 169(4), 2982-2991. https://doi.org/10.1104/pp.15.00717
Bhat, W.W., Lattoo, S.K., Razdan, S., Dhar, N., Rana, S., Dhar, R.S., Khan, S. and Vishwakarma, R.A. 2012. Molecular cloning, bacterial expression and promoter analysis of squalene synthase from Withania somnifera (L.) Dunal. Gene, 499(1), 25-36. https://doi.org/10.1016/j.gene.2012.03.004
Busquets, A., Keim, V., Closa, M., Del Arco, A., Boronat, A., Arró, M. and Ferrer, A. 2008. Arabidopsis thaliana contains a single gene encoding squalene synthase. Plant molecular biology, 67, 25-36. https://doi. org/10.1007/s11103-008-9299-3
Chalbi, N., Martínez-Ballesta, M.C., Youssef, N.B. and Carvajal, M. 2015. Intrinsic stability of Brassicaceae plasma membrane in relation to changes in proteins and lipids as a response to salinity. Journal of Plant Physiology, 175, 148-156. http:// doi.org/10.1016/j.jplph.2014.12.003
Chao, J., Li, Z., Sun, Y., Aluko, O.O., Wu, X., Wang, Q. and Liu, G. 2021. MG2C: A user-friendly online tool for drawing genetic maps. Molecular horticulture, 1, 1-4. https://doi.org/10.1186/s43897-021-00020-x
Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y. and Xia, R. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202. http://doi.org/10.1016/j.molp.2020.06.009
Chen, H., Wang, T., He, X., Cai, X., Lin, R., Liang, J., Wu, J., King, G. and Wang, X. 2022. BRAD V3. 0: an upgraded Brassicaceae database. Nucleic Acids Research, 50(D1), D1432-D1441. https://doi.org/10.1093/nar/gkab1057
Devarenne, T.P., Shin, D.H., Back, K., Yin, S. and Chappell, J. 1998. Molecular characterization of tobacco squalene synthase and regulation in response to fungal elicitor. Archives of Biochemistry and Biophysics, 349(2), 205-215. https://doi.org/10.1002/pld3.63
Essadek, S., Gondcaille, C., Savary, S., Samadi, M., Vamecq, J., Lizard, G., El Kebbaj, R., Latruffe, N., Benani, A., Nasser, B. and Cherkaoui-Malki, M. 2023. Two Argan Oil Phytosterols, Schottenol and Spinasterol, Attenuate Oxidative Stress and Restore LPS-Dysregulated Peroxisomal Functions in Acox1−/− and Wild-Type BV-2 Microglial Cells. Antioxidants, 12(1), 168. https://doi.org/10.3390/antiox12010168
Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. and Rokhsar, D.S. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic acids research, 40(D1), D1178-D1186. https://doi.org/10.1093/nar/gkr944
Hazra, A., Dutta, M., Dutta, R., Bhattacharya, E., Bose, R. and Biswas, S.M. 2023. Squalene synthase in plants–Functional intricacy and evolutionary divergence while retaining a core catalytic structure. Plant Gene, 33, 100403. https://doi.org/10.1016/j.plgene.2023.100403
Hurst, L.D. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. TRENDS in Genetics, 18(9), 486-487. https://doi.org/10.1016/s0168-9525(02)02722-1
Jennings, S.M., Tsay, Y.H., Fisch, T.M. and Robinson, G.W. 1991. Molecular cloning and characterization of the yeast gene for squalene synthetase. Proceedings of the National Academy of Sciences, 88(14), 6038-6042. https://doi.org/10.1073/pnas.88.14.6038
Jiang, Y., Chen, H., Chen, X., Köllner, T.G., Jia, Q., Wymore, T.W., Wang, F. and Chen, F. 2015. Volatile squalene from a nonseed plant Selaginella moellendorffii: emission and biosynthesis. Plant physiology and biochemistry, 96, 1-8. https://doi.org/10.1016/j.plaphy.2015.07.010
Kagale, S., Robinson, S.J., Nixon, J., Xiao, R., Huebert, T., Condie, J., Kessler, D., Clarke, W.E., Edger, P.P., Links, M.G. and Sharpe, A.G. 2014. Polyploid evolution of the Brassicaceae during the Cenozoic era. The Plant Cell, 26(7), 2777-2791. https://doi.org/10.1105/tpc.114.126391
Kim, T.D., Han, J.Y., Huh, G.H. and Choi, Y.E. 2011a. Expression and functional characterization of three squalene synthase genes associated with saponin biosynthesis in Panax ginseng. Plant and Cell Physiology, 52(1), 125-137. https://doi.org/10.1093/pcp/pcq179
Kim, Y.S., Cho, J.H., Park, S., Han, J.Y., Back, K. and Choi, Y.E. 2011b. Gene regulation patterns in triterpene biosynthetic pathway driven by overexpression of squalene synthase and methyl jasmonate elicitation in Bupleurum falcatum. Planta, 233, 343-355. https://doi.org//10.1007/s00425-010-1292-9
Lee, S. and Poulter, C.D. 2008. Cloning, solubilization, and characterization of squalene synthase from Thermosynechococcus elongatus BP-1. Journal of Bacteriology, 190(11), 3808-3816. https://doi.org/10.1128/JB.01939-07
Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P. and Rombauts, S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research, 30(1), 325-327. https://doi.org/10.1093/nar/30.1.325
Liu, D., Pi, J., Zhang, B., Zeng, H., Li, C., Xiao, Z., Fang, F., Liu, M., Deng, N. and Wang, J. 2023. Phytosterol of lotus seed core powder alleviates hypercholesterolemia by regulating gut microbiota in high-cholesterol diet-induced C57BL/6J mice. Food Bioscience, 51, 102279. https://doi.org/10.1016/j.fbio.2022.102279
Lopez-Garcia, G., Cilla, A., Barberá, R. and Alegria, A. 2017. Antiproliferative effect of plant sterols at colonic concentrations on Caco-2 cells. Journal of functional foods, 39, 84-90. https://doi.org/10.1016/j.jff.2017.10.006
López-García, G., Cilla, A., Barberá, R. and Alegría, A. 2020. Anti-inflammatory and cytoprotective effect of plant sterol and galactooligosaccharides-enriched beverages in caco-2 cells. Journal of agricultural and food chemistry, 68(7), 1862-1870. https://doi.org/10.1021/acs.jafc.9b03025
McKenzie, T.L., Jiang, G.U.O.J.I.A.N., Straubhaar, J.R., Conrad, D.G. and Shechter, I. 1992. Molecular cloning, expression, and characterization of the cDNA for the rat hepatic squalene synthase. Journal of Biological Chemistry, 267(30), 21368-21374. https://doi.org/10.1016/S0021-9258(19)36619-0
Nasrollahi, V., Mirzaie-Asl, A., Piri, K., Nazeri, S. and Mehrabi, R. 2014. The effect of drought stress on the expression of key genes involved in the biosynthesis of triterpenoid saponins in liquorice (Glycyrrhiza glabra). Phytochemistry, 103, 32-37. https://doi.org/10.1016/j.phytochem.2014.03.004
Nguyen, H.T., Neelakadan, A.K., Quach, T.N., Valliyodan, B., Kumar, R., Zhang, Z. and Nguyen, H.T. 2013. Molecular characterization of Glycine max squalene synthase genes in seed phytosterol biosynthesis. Plant Physiology and Biochemistry, 73, 23-32. https://doi.org/10.1016/j.plaphy.2013.07.018
Okada, S., Devarenne, T.P. and Chappell, J. 2000. Molecular characterization of squalene synthase from the green microalga Botryococcus braunii, race B. Archives of biochemistry and biophysics, 373(2), 307-317. https://doi.org/10.1006/abbi.1999.1568
Poulose, N., Sajayan, A., Ravindran, A., Chandran, A., Priyadharshini, G.B., Selvin, J. and Kiran, G.S. 2021. Anti-diabetic potential of a stigmasterol from the seaweed Gelidium spinosum and its application in the formulation of nanoemulsion conjugate for the development of functional biscuits. Frontiers in nutrition, 8, 694362. https://doi.org/10.3389/fnut.2021.694362
Poulter, C.D. 1990. Biosynthesis of non-head-to-tail terpenes. Formation of 1'-1 and 1'-3 linkages. Accounts of Chemical Research, 23(3), 70-77. https://doi.org/10.1021/ar00171a003
Rhee, S.Y., Beavis, W., Berardini, T.Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M. and Miller, N. 2003. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic acids research, 31(1), 224-228. https://doi.org/10.1093/nar/gkg076
Rilling, H.C. and Epstein, W.W. 1969. Mechanism of squalene biosynthesis. Presqualene, a pyrophosphorylated precursor to squalene. Journal of the American Chemical Society, 91(4), 1041-1042. https://doi.org/10.1021/ja01032a052
Robinson, G.W., Tsay, Y.H., Kienzle, B.K., Smith-Monroy, C.A. and Bishop, R.W. 1993. Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation. Molecular and Cellular Biology, 13(5), 2706-2717. https://doi.org/10.1128/mcb.13.5.2706
Rong, Q., Jiang, D., Chen, Y., Shen, Y., Yuan, Q., Lin, H., Zha, L., Zhang, Y. and Huang, L. 2016. Molecular cloning and functional analysis of squalene synthase 2 (SQS2) in Salvia miltiorrhiza Bunge. Frontiers in Plant Science, 7, 1274. https://doi.org/10.3389/fpls.2016.01274
Rossi, S. and Huang, B. 2022. Sitosterol-mediated antioxidant regulation to enhance heat tolerance in creeping bentgrass. Journal of the American Society for Horticultural Science, 147(1), 18-24. https://doi.org/10.21273/JASHS05107-21
Sheikhi, S., Ebrahimi, A., Heidari, P., Amerian, M.R., Rashidi-Monfared, S. and Alipour, H. 2023. Exogenous 24-epibrassinolide ameliorates tolerance to high-temperature by adjusting the biosynthesis of pigments, enzymatic, non-enzymatic antioxidants, and diosgenin content in fenugreek. Scientific Reports, 13(1), 6661. https://doi.org/10.1038/s41598-023-33913-6
Shirazi, Z., Aalami, A., Tohidfar, M. and Sohani, M.M. 2019. Triterpenoid gene expression and phytochemical content in Iranian licorice under salinity stress. Protoplasma, 256, 827-837. https://doi.org/10.1007/s00709-018-01340-4
Singh, A.K., Dwivedi, V., Rai, A., Pal, S., Reddy, S.G.E., Rao, D.K.V., Shasany, A.K. and Nagegowda, D.A. 2015. Virus‐induced gene silencing of Withania somnifera squalene synthase negatively regulates sterol and defence‐related genes resulting in reduced withanolides and biotic stress tolerance. Plant biotechnology journal, 13(9), 1287-1299. https://doi.org /10.1111/pbi.12347
Summers, C., Karst, F. and Charles, A.D. 1993. Cloning, expression and characterisation of the cDNA encoding human hepatic squalene synthase, and its relationship to phytoene synthase. Gene, 136(1-2), 185-192. https://doi.org/10.1016/0378-1119(93)90462-c.
Wang, H., Nagegowda, D.A., Rawat, R., Bouvier‐Navé, P., Guo, D., Bach, T.J. and Chye, M.L. 2012a. Overexpression of Brassica juncea wild‐type and mutant HMG‐CoA synthase 1 in Arabidopsis up‐regulates genes in sterol biosynthesis and enhances sterol production and stress tolerance. Plant biotechnology journal, 10(1), 31-42. http://doi.org/10.1111/j.1467-7652.2011.00631.x
Wang, K., Senthil-Kumar, M., Ryu, C.M., Kang, L. and Mysore, K.S. 2012b. Phytosterols play a key role in plant innate immunity against bacterial pathogens by regulating nutrient efflux into the apoplast. Plant physiology, 158(4), 789-1802. http:// doi.org/10.1104/pp.111.189217
Wang, S., Wang, X., Liu, Z., Sun, T. and Zou, L. 2022. Expression analysis of squalene synthase gene in mevalonate pathway of Sanghuangporus baumii. Biotechnology & Biotechnological Equipment, 36(1), 176-183. https://doi.org/10.1080/13102818.2022.2060759
Wei, S., Yang, X., Huo, G., Ge, G., Liu, H., Luo, L., Hu, J., Huang, D. and Long, P. 2020. Distinct metabolome changes during seed germination of lettuce (Lactuca sativa L.) in response to thermal stress as revealed by untargeted metabolomics analysis. International Journal of Molecular Sciences, 21(4), 1481. https://doi.org/10.3390/ijms21041481
Zhang, B., Liu, Y., Chen, M., Feng, J., Ma, Z., Zhang, X. and Zhu, C. 2018. Cloning, expression analysis and functional characterization of squalene synthase (SQS) from Tripterygium wilfordii. Molecules, 23(2), 269. https://doi.org/10.3390/molecules23020269
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Rajkumar Bangkim, Komal Chaudhary, Priya Panjabi
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
