Peroxidase-Mediated Thymoquinone Biosynthesis in Nigella sativa: A pH-Dependent Enzymatic Insight
Author Affiliations
- 1Department of Biotechnology, School of Life Sciences, Mahatma Gandhi Central University, Motihari-845401, India
- 2Department of Biotechnology, School of Life Sciences, Mahatma Gandhi Central University, Motihari-845401, India
Res. J. Recent Sci., Volume 15, Issue (1), Pages 5-10, January,2 (2026)
Abstract
Nigella sativa (N. sativa) is widely recognized for its pharmacological potential, largely attributed to thymoquinone (TQ), a key bioactive compound. Although TQ biosynthesis has been reported in various plants and microorganisms, its enzymatic pathway in N. sativa remains inadequately characterized. This study investigates the role of peroxidase enzymes in TQ biosynthesis, using thymol-a known precursoras the substrate, hypothesizing that the antioxidant capacity of N. sativa arises from robust enzymatic defense mechanisms. Peroxidase activity was evaluated in the leaves, buds, and fruits of the Rajendra Shyama cultivar using 1% hydrogen peroxide (H₂O₂) in Tris buffer at different pH 6.5, 7.0 and 7.5. Absorbance analyses at 254 nm and 274 nm were used to monitor TQ and thymol formation, respectively. Results revealed plant part-specific variations in enzymatic activity, with leaves unveiling the highest and fruits the lowest peroxidase activity. Optimal activity was observed at pH 6.5, which suggests a preference for slightly acidic to neutral conditions for effective TQ biosynthesis. Notably, differential absorbance patterns and correlation studies indicate the possible involvement of metabolites other than thymol in the biosynthetic pathway. These findings provide new insights into the enzymatic dynamics of N. sativa, with significant implications for therapeutic exploitation and metabolic engineering.
References
- Amin, B., & Hosseinzadeh, H. (2016)., Black cumin (Nigella sativa) and its active constituent, thymoquinone: an overview on the analgesic and anti-inflammatory effects., Planta medica, 82 (01/02), 8-16.
- Paarakh, P. M. (2010)., Nigella sativa Linn.–A comprehensive review., Indian journal of natural products and resources, 1(4), 409-429.
- Yimer, E. M., Tuem, K. B., Karim, A., Ur-Rehman, N., & Anwar, F. (2019)., Nigella sativa L. (Black Cumin): A Promising Natural Remedy for Wide Range of Illnesses., Evidence-based complementary and alternative medicine : eCAM, 2019, 1528635. https://doi.org/10.1155/ 2019/1528635
- Khan, M. A. (1999). Chemical composition and medicinal properties of Nigella sativa Linn. Inflammopharmacology, 7(1), 15-35. https://doi.org/10. 1007/s10787-999-0023-y., undefined, undefined
- Randhawa, M. A. & Alghamdi, M. S. (2011)., Anticancer activity of Nigella sativa (black seed)—a review., The American journal of Chinese medicine, 39(06), 1075-1091. https://doi.org/10.1142/S0192415X1100941X.
- Darakhshan, S., Pour, A. B., Colagar, A. H., & Sisakhtnezhad, S. (2015)., Thymoquinone and its therapeutic potentials., Pharmacological research, 95, 138-158. https://doi.org/10.1016/j.phrs.2015.03.011.
- Ahmad, A., Mishra, R. K., Vyawahare, A., Kumar, A., Rehman, M. U., Qamar, W., Khan, A. Q., & Khan, R. (2019)., Thymoquinone (2-Isoprpyl-5-methyl-1, 4-benzoquinone) as a chemopreventive/anticancer agent: Chemistry and biological effects., Saudi pharmaceutical journal, 27(8), 1113–1126. https://doi.org/10.1016/j.jsps. 2019.09.008.
- Ahmad, A., Husain, A., Mujeeb, M., Khan, S. A., Najmi, A. K., Siddique, N. A., Damanhouri, Z. A., & Anwar, F. (2013)., A review on therapeutic potential of Nigella sativa: A miracle herb., Asian Pacific journal of tropical biomedicine, 3(5), 337–352. https://doi.org/10.1016/S2221-1691(13)60075-1.
- Isaev, N. K., Genrikhs, E. E., & Stelmashook, E. V. (2023)., Antioxidant Thymoquinone and Its Potential in the Treatment of Neurological Diseases., Antioxidants, 12(2), 433. https://doi.org/10.3390/antiox12020433.
- Soliman, R. M., Salam, R. A. A., Eid, B. G., Khayyat, A., Neamatallah, T., Mesbah, M. K., & Hadad, G. M. (2020)., Stability study of thymoquinone, carvacrol and thymol using HPLC-UV and LC-ESI-MS., Acta Pharmaceutica, 70(3), 325-342. https://doi.org/10.2478/acph-2020-0028.
- Salehi, B., Mishra, A. P., Nigam, M., Sener, B., Kilic, M., Sharifi-Rad, M., Fokou, P. V. T., Martins, N., & Sharifi-Rad, J. (2018)., Resveratrol: A Double-Edged Sword in Health Benefits., Biomedicines, 6(3), 91. https://doi.org/ 10.3390/biomedicines6030091.
- Ringer, K. L., Davis, E. M., & Croteau, R. (2005)., Monoterpene metabolism. Cloning, expression, and characterization of (−)-isopiperitenol / (−)-carveol dehydrogenase of peppermint and spearmint., Plant physiology, 137(3), 863-872. https://doi.org/10.1104/pp. 104.053298.
- Youn, H. D., Kim, E. J., Roe, J. H., Hah, Y. C., & Kang, S. O. (1996)., A novel nickel-containing superoxide dismutase from Streptomyces spp., The Biochemical journal, 318(3), 889–896. https://doi.org/10.1042/bj3180 889.
- Lüddeke, F., Wülfing, A., Timke, M., Germer, F., Weber, J., Dikfidan, A. & Harder, J. (2012)., Geraniol and geranial dehydrogenases induced in anaerobic monoterpene degradation by Castellaniella defragrans., Applied and environmental microbiology, 78(7), 2128-2136. https://doi.org/10.1128/AEM.07226-11.
- Černý, M., Habánová, H., Berka, M., Luklová, M., & Brzobohatý, B. (2018)., Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks., International journal of molecular sciences, 19(9), 2812. https://doi.org/10.3390/ijms19092 812.
- Al-Khayri, J. M., Rashmi, R., Toppo, V., Chole, P. B., Banadka, A., Sudheer, W. N., Nagella, P., Shehata, W. F., Al-Mssallem, M. Q., Alessa, F. M., Almaghasla, M. I., & Rezk, A. A. (2023)., Plant Secondary Metabolites: The Weapons for Biotic Stress Management., Metabolites, 13(6), 716. https://doi.org/10.3390/metabo 13060716.
- Freitas, C. D. T., Costa, J. H., Germano, T. A., de O Rocha, R., Ramos, M. V., & Bezerra, L. P. (2024)., Class III plant peroxidases: From classification to physiological functions., International journal of biological macromolecules, 263(1), 130306. https://doi.org/10.1016/ j.ijbiomac.2024.130306.
- Alamri, M. A., Abdel-Kader, M. S., Salkini, M. A., & Alamri, M. A. (2024)., Thymol and carvacrol derivatives as anticancer agents; synthesis, in vitro activity, and computational analysis of biological targets., RSC advances, 14(42), 30662–30672. https://doi.org/10.1039/ d4ra03941f.
- Handy, D. E., & Loscalzo, J. (2022)., The role of glutathione peroxidase-1 in health and disease., Free radical biology & medicine, 188, 146–161. https://doi.org/10.1016/j.freeradbiomed.2022.06.004.
- Rasuli, N., Riahi, H., Shariatmadari, Z., Nohooji, M. G., MehrabanJoubani, P., & Dehestani, A. (2025)., Enhancing thymol and carvacrol biosynthesis in Thymus vulgaris L. using Laurencia caspica seaweed extract: Biostimulant potential and gene expression insights., Journal of Applied Phycology, 37(1), 645-657. https://doi.org/10.21203/rs.3.rs-4626550/v1.
- Jiang, B., Duan, D., Gao, L., Zhou, M., Fan, K., Tang, Y., Xi, J., Bi, Y., Tong, Z., Gao, G. F., et al. (2024)., Properties and Applications of Plant Peroxidases., Journal of Biochemical Technology, 15(4), 3-8. https://doi.org/10.51847/6C0QKTK3Na.
- Botnick, I., Xue, W., Bar, E., Ibdah, M., Schwartz, A., Joel, D. M., Lev, E., Fait, A., & Lewinsohn, E. (2012)., Distribution of Primary and Specialized Metabolites in Nigella sativa Seeds, a Spice with Vast Traditional and Historical Uses., Molecules, 17(9), 10159-10177. https://doi.org/10.3390/molecules170910159.
- Rudolph, K., Parthier, C., Egerer-Sieber, C., Geiger, D., Muller, Y. A., Kreis, W., & Müller-Uri, F. (2016)., Expression, crystallization and structure elucidation of γ-terpinene synthase from Thymus vulgaris., Acta crystallographica. Section F, Structural biology communications, 72(1), 16–23. https://doi.org/10.1107/ S2053230X15023043.
- Pandey, V. P., Singh, S., Singh, R., & Dwivedi, U. N. (2012)., Purification and characterization of peroxidase from papaya (Carica papaya) fruit., Applied biochemistry and biotechnology, 167(2), 367-376. https://doi.org/10. 1007/s12010-012-9672-1.
- Naghdi Badi, H. A., Abdollahi, M., Mehrafarin, A., Ghorbanpour, M., Tolyat, S. M., Qaderi, A., & Ghiaci Yekta, M. (2017)., An overview on two valuable natural and bioactive compounds, thymol and carvacrol, in medicinal plants., Journal of Medicinal Plants, 16(63), 1-32.
- Kainat, R., Mushtaq, Z., & Nadeem, F. (2019)., Derivatization of essential oil of Eucalyptus to obtain valuable market products-A comprehensive review., International Journal of Chemical and Biochemical Sciences. 15, 58-68.
- Bradford, M. M. (1976)., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding., Analytical Biochemistry, 72(1-2), 248–254.
- Krause, S. T., Liao, P., Crocoll, C., Boachon, B., Förster, C., Leidecker, F., Wiese, N., Zhao, D., Wood, J. C., Buell, C. R., Gershenzon, J., Dudareva, N., & Degenhardt, J. (2021)., The biosynthesis of thymol, carvacrol, and thymohydroquinone in Lamiaceae proceeds via cytochrome P450s and a short-chain dehydrogenase., Proceedings of the National Academy of Sciences of the United States of America, 118(52), e2110092118. https://doi.org/10.1073/ pnas.2110092118.
- Sadeghi, E., Imenshahidi, M., & Hosseinzadeh, H. (2023)., Molecular mechanisms and signaling pathways of black cumin (Nigella sativa) and its active constituent, thymoquinone: a review., Molecular biology reports, 50(6), 5439–5454. https://doi.org/10.1007/s11033-023-08363-y.
- Shaukat, A., Zaidi, A., Anwar, H., & Kizilbash, N. (2023)., Mechanism of the antidiabetic action of Nigella sativa and Thymoquinone: a review., Frontiers in Nutrition, 10, 1126272. https://doi.org/10.3389/fnut.2023.1126272.
- Zhou, W., Zhang, Y., Li, R., Peng, S., Ruan, R., Li, J., & Liu, W. (2021)., Fabrication of Caseinate Stabilized Thymol Nanosuspensions via the pH-Driven Method: Enhancement in Water Solubility of Thymol., Foods, 10(5), 1074. https://doi.org/10.3390/foods10051074.
- BenchChem Technical Support Team (2025). Stability of chlorothymol: An in-depth technical guide on pH and temperature effects. BenchChem. Online pdf. Available at: https://www.benchchem.com/pdf/Stability_of_Chlorothymol_An_In_depth_Technical_Guide_on_pH_and_Temperature_Effects.pdf. December 2025., undefined, undefined
- Helmenstine, A. (2020)., pH Indicator Chart—Colors and Ranges., Science Notes.
- Gyaneshwari, U., & Pandey, B. (2024)., Tracing metabolic route of thymoquinone biosynthesis in diverse Nigella sativa L. cultivars using RP-HPLC technique., Industrial Crops and Products, 219, 118972. https://doi.org/10.1016/j.indcrop.2024.118972.
- Cheng, R., Yang, S., Wang, D., Qin, F., Wang, S., & Meng, S. (2025)., Advances in the Biosynthesis of Plant Terpenoids: Models, Mechanisms, and Applications., Plants, 14(10), 1428. https://doi.org/ 10.3390/plants14101428.
- Zhu, J., Zhang, Y., Jiang, H., Zheng, M., & Gong, Y. (2025)., Engineering the oleaginous yeast Yarrowia lipolytica for co-production of phenolic monoterpenes thymol and carvacrol., Microbial cell factories, 24(1), 208. https://doi.org/10.1186/s12934-025-02836-4.
- Kim, E., Kim, M., & Oh, M. K. (2024)., Whole-cell bioconversion for producing thymoquinone by engineered Saccharomyces cerevisiae., Enzyme and Microbial Technology, 178, 110455. https://doi.org/10.1016/ j.enzmictec.2024.110455.
- Zhang, L., Chen, W., Lu, Y., Jiang, Y., Lin, L., Li, S., ... & Wang, S. (2025)., Electrooxidation of Thymol or Carvacrol to Obtain Thymoquinone on Defective Pt/CeO2 Catalyst., Advanced Functional Materials, 2424617. https://doi.org/10.1002/adfm.202424617.
- Zheng, Y., Peng, Y., Zhao, S., Li, X., Xie, Z., Tan, R., Yang, L., & Jiang, H. (2025)., Comprehensive genome-wide analysis of peroxidase gene family in the Herpetospermum pedunculosum identifies HpPRX involved in lignan-specific biosynthesis., International journal of biological macromolecules, 318(3), 145120. https://doi.org/10.1016/ j.ijbiomac.2025.145120.
- Lu Y, Ma R, Wu K, Sun J, Li Y, Zhao J, Qi Z, Sha G, Ge H, Shi Y. (2025)., Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica)., PeerJ, 13, e19741. https://doi.org/10.7717/peerj.19741.
