Academic Journal
Stage-Resolved Proteomic and Structural Insights Into Apocarotenoid Biosynthesis During Saffron (Crocus sativus) Flower Development.
| Τίτλος: | Stage-Resolved Proteomic and Structural Insights Into Apocarotenoid Biosynthesis During Saffron (Crocus sativus) Flower Development. |
|---|---|
| Συγγραφείς: | Muduli N; Plant Molecular Biology and Biotechnology Lab, Department of Botany, Ravenshaw University, Cuttack, India.; Centre of Excellence for Environment & Public Health, Ravenshaw University, Cuttack, India., Mohan Behera P; Centre of Excellence for Environment & Public Health, Ravenshaw University, Cuttack, India.; Redox Biology and Proteomics Lab, Department of Zoology, Ravenshaw University, Cuttack, India., Sahoo S; Plant Molecular Biology and Biotechnology Lab, Department of Botany, Ravenshaw University, Cuttack, India.; Centre of Excellence for Environment & Public Health, Ravenshaw University, Cuttack, India., Samanta L; Centre of Excellence for Environment & Public Health, Ravenshaw University, Cuttack, India.; Redox Biology and Proteomics Lab, Department of Zoology, Ravenshaw University, Cuttack, India., Kumar Sahoo K; Plant Molecular Biology and Biotechnology Lab, Department of Botany, Ravenshaw University, Cuttack, India.; Centre of Excellence for Environment & Public Health, Ravenshaw University, Cuttack, India. |
| Πηγή: | Proteomics [Proteomics] 2026 Oct; Vol. 26 (10), pp. 46-59. Date of Electronic Publication: 2026 May 30. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101092707 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1615-9861 (Electronic) Linking ISSN: 16159853 NLM ISO Abbreviation: Proteomics Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Weinheim, Germany : Wiley-VCH |
| Ιατρικοί όροι (MeSH): | Crocus*/metabolism , Crocus*/growth & development , Crocus*/genetics , Flowers*/growth & development , Flowers*/metabolism , Flowers*/genetics , Plant Proteins*/metabolism , Plant Proteins*/genetics , Plant Proteins*/chemistry , Proteome*/metabolism , Proteome*/analysis, Proteomics/methods ; Carotenoids/metabolism ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Tandem Mass Spectrometry ; Protein Interaction Maps |
| Περίληψη: | Saffron (Crocus sativus L.) is one of the world's most valuable spices, renowned for its distinctive aroma, flavor, and pharmacological properties derived from apocarotenoids such as crocin, picrocrocin, and safranal, which accumulate in the stigmas during flower development. Despite their economic and medicinal importance, the molecular regulation of apocarotenoid biosynthesis across floral developmental stages remains poorly understood, particularly at the proteomic level. To address this gap, we applied an LC-MS/MS-based proteomic approach combined with bioinformatic and structural analyses to characterize stage-specific protein expression across five developmental stages: corm with floral shoot buds (A1), flower inside the sheath (S1), just outside the sheath (S2), flower at unopened state (S3), and flower at opened state (S4). Differential abundance analysis, gene ontology enrichment, STRING-based protein-protein interaction networks, KEGG pathway mapping, and structural modeling identified 57 developmentally regulated proteins linked to stigma differentiation and apocarotenoid metabolism. Stage-specific protein sets comprising 128 (A1), 44 (S1), 38 (S2), 29 (S3), and 29 (S4) proteins were selected using stringent statistical thresholds and validated through Limma-based differential expression analysis. Key enzymes, including PSY2, CCD2, ALDH2B4, and UGT707B1, emerged as central regulators of apocarotenoid biosynthesis during floral maturation. Overall, this study provides a comprehensive proteomic framework underlying stigma development and apocarotenoid accumulation in saffron, offering valuable molecular targets for improving metabolite yield and quality. The data supporting this study have been deposited in the ProteomeXchange repository under the identifier PXD076029. (© 2026 Wiley‐VCH GmbH.) |
| References: | N. Esmaeili, H. Ebrahimzadeh, K. Abdi, and S. Safarian, “Determination of Some Phenolic Compounds in Crocus sativus L. Corms and Its Antioxidant Activities Study,” Pharmacognosy Magazine 7, no. 25 (2011): 74–80. B. Javadi, A. Sahebkar, and S. A. Emami, “A Survey on Saffron in Major Islamic Traditional Medicine Books,” Iranian Journal of Basic Medical Sciences 16, no. 1 (2013): 1–11. C. Pintado, A. de Miguel, O. Acevedo, L. Nozal, J. L. Novella, and R. Rotger, “Bactericidal Effect of Saffron (Crocus sativus L.) on Salmonella Enterica During Storage,” Food Control 22, no. 3‐4 (2011): 638–642. H. Hosseinzadeh and H. M. Younesi, “Antinociceptive and Anti‐Inflammatory Effects of Crocus sativus L. Stigma and Petal Extracts in Mice,” BMC Pharmacology 2 (2002): 1–8. H. Yaribeygi, V. Zare, A. E. Butler, G. E. Barreto, and A. Sahebkar, “Antidiabetic Potential of Saffron and Its Active Constituents,” Journal of Cellular Physiology 234, no. 6 (2019): 8610–8617. J. P. Melnyk, S. Wang, and M. F. Marcone, “Chemical and Biological Properties of the World's Most Expensive Spice: Saffron,” Food Research International 43, no. 8 (2010): 1981–1989. M. H. Walter and D. Strack, “Carotenoids and Their Cleavage Products: Biosynthesis and Functions,” Natural Product Reports 28, no. 4 (2011): 663. C. Jr and E. Gantt, “Genes and Enzymes of Carotenoid Biosynthesis in Plants,” Annual Review of Plant Biology 49, no. 1 (1998): 557–583. X. Qian, Y. Sun, G. Zhou, et al., “Single‐Molecule Real‐Time Transcript Sequencing Identified Flowering Regulatory Genes in Crocus sativus,” BMC Genomics [Electronic Resource] 20 (2019): 1–18. J. Hu, Y. Liu, X. Tang, et al., “Transcriptome Profiling of the Flowering Transition in Saffron,” Scientific Reports 10, no. 1 (2020): 9680. A. Chaudhary and K. Singh, “Transcriptome Analysis of Apical Meristem Enriched Bud Samples for Size Dependent Flowering Commitment in Crocus sativus Reveal Role of Sugar and Auxin Signalling,” Molecular Biology Reports 51, no. 1 (2024): 605. T. Maier, M. Güell, and L. Serrano, “Correlation of mRNA and Protein in Complex Biological Samples,” FEBS Letters 583, no. 24 (2009): 3966–3973. B. Schwanhäusser, D. Busse, N. Li, et al., “Global Quantification of Mammalian Gene Expression Control,” Nature 473, no. 7347 (2011): 337–342. J. K. Rose, S. Bashir, J. J. Giovannoni, M. M. Jahn, and R. S. Saravanan, “Tackling the Plant Proteome: Practical Approaches, Hurdles and Experimental Tools,” The Plant Journal 39, no. 5 (2004): 715–733. M. Wilkins, “Proteomics Data Mining,” Expert Review of Proteomics 6, no. 6 (2009): 599–603. L. Gómez Gómez, L. Morote, S. Frusciante, et al., “Fortification and Bioaccessibility of Saffron Apocarotenoids in Potato Tubers,” Frontiers in Nutrition 9 (2022): 1045979. J. Chen, G. Zhou, Y. Dong, et al., “Screening of Key Proteins Affecting Floral Initiation of Saffron Under Cold Stress Using iTRAQ‐Based Proteomics,” Frontiers in Plant Science 12 (2021): 644934. G. Sharifi, H. Ebrahimzadeh, B. Ghareyazie, J. Gharechahi, and E. Vatankhah, “Identification of Differentially Accumulated Proteins Associated With Embryogenic and Non‐Embryogenic Calli in Saffron (Crocus sativus L.),” Proteome Science 10, no. 1 (2012): 3. M. Eftekhari, M. G. Javid, S. Aliniaeifard, and S. Nicola, “Alteration of Flower Yield and Phytochemical Compounds of Saffron (Crocus sativus L.) by Application of Different Light Qualities and Growth Regulators,” Horticulturae 9, no. 2 (2023): 169. R. V. Molina, M. Valero, Y. Navarro, J. L. Guardiola, and A. J. S. H. Garcia‐Luis, “Temperature Effects on Flower Formation in Saffron (Crocus sativus L.),” Scientia Horticulturae 103, no. 3 (2005): 361–379. W. J. Hurkman and C. K. Tanaka, “Solubilization of Plant Membrane Proteins for Analysis by Two‐Dimensional Gel Electrophoresis,” Plant physiology 81, no. 3 (1986): 802–806. M. M. Bradford, “A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein‐Dye Binding,” Analytical Biochemistry 72, no. 1‐2 (1976): 248–254. The UniProt Consortium. “The Universal Protein Resource (UniProt),” Nucleic Acids Research 33 (2008): D190–195. R. G. Sadygov, “Using SEQUEST With Theoretically Complete Sequence Databases,” Journal of the American Society for Mass Spectrometry 26, no. 11 (2015): 1858–1864. V. Dorfer, P. Pichler, T. Stranzl, et al., “MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra,” Journal of Proteome Research 13, no. 8 (2014): 3679–3684. B. C. Orsburn, “Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics,” Proteomes 9, no. 1 (2021): 15. D. Salvachúa, A. T. Martínez, M. Tien, et al., “Differential Proteomic Analysis of the Secretome of Irpex lacteus and Other White‐Rot Fungi During Wheat Straw Pretreatment,” Biotechnology for Biofuels 6 (2013): 1–14. D. Szklarczyk, A. L. Gable, K. C. Nastou, et al., “The STRING Database in 2021: Customizable Protein–Protein Networks, and Functional Characterization of User‐Uploaded Gene/Measurement Sets,” Nucleic Acids Research 49, no. D1 (2021): D605–D612. D. Szklarczyk, R. Kirsch, M. Koutrouli, et al., “The STRING Database in 2023: Protein–Protein Association Networks and Functional Enrichment Analyses for any Sequenced Genome of Interest,” Nucleic Acids Research 51, no. D1 (2023): D638–D646. J. C. Oliveros, VENNY An Interactive Tool for Comparing Lists With Venn Diagrams (2007), http://bioinfogp.cnb.csic.es/tools/venny/index.html. M. E. Ritchie, B. Phipson, D. I. Wu, Y. Hu, C. W. Law, and W. Shi, “Limma Powers Differential Expression Analyses for RNA‐Sequencing and Microarray Studies,” Nucleic Acids Research 43, no. 7 (2015): e47–e47. M. Kanehisa and S. Goto, “KEGG: Kyoto Encyclopedia of Genes and Genomes,” Nucleic Acids Research 28, no. 1 (2000): 27–30. S. X. Ge, D. Jung, and R. Yao, “ShinyGO: A Graphical Gene‐Set Enrichment Tool for Animals and Plants,” Bioinformatics 36, no. 8 (2020): 2628–2629. H. M. Berman, J. Westbrook, Z. Feng, et al., “The Protein Data Bank,” Nucleic Acids Research 28, no. 1 (2000): 235–242. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic Local Alignment Search Tool,” Journal of Molecular Biology 215, no. 3 (1990): 403–410. B. Webb and A. Sali, “Comparative Protein Structure Modeling Using MODELLER,” Current Protocols in Bioinformatics 54, no. 1 (2016): 5–6. M. A. Martí‐Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Šali, “Comparative Protein Structure Modeling of Genes and Genomes,” Annual Review of Biophysics and Biomolecular Structure 29, no. 1 (2000): 291–325. S. Khan, A. F. Alvi, S. Saify, N. Iqbal, and N. A. Khan, “The Ethylene Biosynthetic Enzymes, 1‐aminocyclopropane‐1‐carboxylate (ACC) Synthase (ACS) and ACC Oxidase (ACO): The Less Explored Players in Abiotic Stress Tolerance,” Biomolecules 14, no. 1 (2024): 90. Q. Wang, M. Wang, Z. Zhang, et al., “McACO2 Gene Promotes Ethylene‐Mediated Scopoletin Biosynthesis in Noni (Morinda citrifolia),” Plant and Cell Physiology 66 (2025): 1839–1855. H. Zhang, S. Li, L. Yang, et al., “Gain‐of‐Function of the 1‐aminocyclopropane‐1‐carboxylate Synthase Gene ACS1G Induces Female Flower Development in Cucumber Gynoecy,” The Plant Cell 33, no. 2 (2021): 306–321. H. Chen, J. Sun, S. Li, et al., “An ACC Oxidase Gene Essential for Cucumber Carpel Development,” Molecular Plant 9, no. 9 (2016): 1315–1327. M. H. Thakuri, U. Chettry, J. Pathak, and N. K. Chrungoo, “Integration of Apocarotenoid and Transcriptome Profiles of Developing Stigmas of Saffron (Crocus sativus L.) Reveals a Multifaceted Control Involving PSY2, OR‐a, PIF1 and HY5 Genes in Regulation of Apocarotenoid Biosynthesis,” South African Journal of Botany 167 (2024): 467–475. O. Ahrazem, A. Rubio‐Moraga, J. Argandona‐Picazo, R. Castillo, and L. Gómez‐Gómez, “Intron Retention and Rhythmic Diel Pattern Regulation of Carotenoid Cleavage Dioxygenase 2 During Crocetin Biosynthesis in Saffron,” Plant Molecular Biology 91, no. 3 (2016): 355–374. M. Guo, Y. Yao, K. Yin, et al., “ACBP4‐WRKY70‐ RAP2.12 Module Positively Regulates Submergence‐Induced Hypoxia Response in Arabidopsis thaliana,” Journal of Integrative Plant Biology 66, no. 6 (2024): 1052–1067. J. G. Donaldson and C. L. Jackson, “ARF Family G proteins and Their Regulators: Roles in Membrane Transport, Development and Disease,” Nature Reviews Molecular Cell Biology 12 (2011): 362–375. M. Huang, M. Yuan, C. Sun, et al., “Roles of AGD2a in Plant Development and Microbial Interactions of Lotus japonicus,” International Journal of Molecular Sciences 23, no. 12 (2022): 6863. R. Caroca, K. A. Howell, I. Malinova, et al., “Knockdown of the Plastid‐Encoded Acetyl‐CoA Carboxylase Gene Uncovers Functions in Metabolism and Development,” Plant Physiology 185, no. 3 (2021): 1091–1110. E. Isono, Y. Saeki, H. Yokosawa, and A. Toh‐e, “Rpn7 Is Required for the Structural Integrity of the 26 S Proteasome of Saccharomyces cerevisiae,” The Journal of Biological Chemistry 279, no. 26 (2004): 27168–27176. J. Kurepa, S. Wang, Y. Li, D. Zaitlin, A. J. Pierce, and J. A. Smalle, “Loss of 26S Proteasome Function Leads to Increased Cell Size and Decreased Cell Number in Arabidopsis Shoot Organs,” Plant Physiology 150, no. 1 (2009): 178–189. Y. Kato and W. Sakamoto, “FtsH Protease in the Thylakoid Membrane: Physiological Functions and the Regulation of Protease Activity,” Frontiers in Plant Science 9 (2018): 855. K. Xu, N. Li, Y. Zhang, et al., “Silencing of Pepper CaFtsH1 or CaFtsH8 Genes Alters Normal Leaf Development,” International Journal of Molecular Sciences 24, no. 5 (2023): 4927. Y. Onda, A. Nagamine, M. Sakurai, T. Kumamaru, M. Ogawa, and Y. Kawagoe, “Distinct Roles of Protein Disulfide Isomerase and P5 Sulfhydryl Oxidoreductases in Multiple Pathways for Oxidation of Structurally Diverse Storage Proteins in Rice,” The Plant Cell 23, no. 1 (2011): 210–223. Q. Sun, E. Duan, R. Jing, et al., “The bZIP Transcription Factor RISBZ1 Balances Grain Filling and ER Stress Response in Rice Grains,” Plant Communications 6, no. 9 (2025): 101458. Z. Xu, S. Chen, Y. Wang, et al., “Crocus Genome Reveals the Evolutionary Origin of Crocin Biosynthesis,” Acta Pharmaceutica Sinica 14, no. 4 (2024): 1878–1891. C. Ampomah‐Dwamena, N. Driedonks, D. Lewis, et al., “The Phytoene Synthase Gene family of Apple (Malus x domestica) and Its Role in Controlling Fruit Carotenoid Content,” BMC Plant Biology 15, no. 1 (2015): 185. M. Ezquerro, E. Burbano‐Erazo, and M. Rodriguez‐Concepcion, “Overlapping and Specialized Roles of Tomato Phytoene Synthases in Carotenoid and Abscisic Acid Production,” Plant Physiology 193, no. 3 (2023): 2021–2036. Z. Wang, L. Zhang, C. Dong, et al., “Characterization and Functional Analysis of Phytoene Synthase Gene Family in Tobacco,” BMC Plant Biology 21, no. 1 (2021): 32. J. G. Lashbrooke, P. R. Young, S. J. Dockrall, K. Vasanth, and M. A. Vivier, “Functional Characterisation of Three Members of the Vitis vinifera L. Carotenoid Cleavage Dioxygenase Gene family,” BMC Plant Biology 13, no. 1 (2013): 156. Z. Sun, J. Hans, M. H. Walter, et al., “Cloning and Characterisation of a Maize Carotenoid Cleavage Dioxygenase (ZmCCD1) and Its Involvement in the Biosynthesis of Apocarotenoids With Various Roles in Mutualistic and Parasitic Interactions,” Planta 228, no. 5 (2008): 789–801. S. Frusciante, G. Diretto, and M. Bruno, Novel Carotenoid Cleavage Dioxygenase Catalyzes the First Dedicated Step in Saffron Crocin Biosynthesis (Proceedings of the National Academy of Sciences of the United States of America, 2014), 12246–12251. M. Masopustová, A. Goga, M. Soural, M. Kopečná, and M. Šebela, “N‐carboxyacyl and N‐α‐aminoacyl Derivatives of Aminoaldehydes as Shared Substrates of Plant Aldehyde Dehydrogenases 10 and 7,” Amino Acids 56, no. 1 (2024): 52. G. Diretto, A. J. López‐Jiménez, O. Ahrazem, et al., “Identification and Characterization of Apocarotenoid Modifiers and Carotenogenic Enzymes for Biosynthesis of Crocins in Buddleja davidii flowers,” Journal of Experimental Botany 72, no. 8 (2021): 3200–3218. A. Trapero, O. Ahrazem, A. Rubio‐Moraga, M. L. Jimeno, M. D. Gómez, and L. Gómez‐Gómez, “Characterization of a Glucosyltransferase Enzyme Involved in the Formation of Kaempferol and Quercetin Sophorosides in Crocus sativus,” Plant Physiology 159, no. 4 (2012): 1335–1354. O. Ahrazem, A. Rubio‐Moraga, A. T. Mozos, and M. L. Gómez‐Gómez, “Genomic Organization of a UDP‐Glucosyltransferase Gene Determines Differential Accumulation of Specific Flavonoid Glucosides in Tepals,” Plant Cell, Tissue and Organ Culture 119, no. 2 (2014): 227–245. |
| Grant Information: | EMR/2016/003094 Science and Engineering Research Board (SERB); Ref.No.-SR/FST/LS/II/2018/219 DST- FIST, Govt. of India; Ref.No.-26913/HED/HE-PTC-WB-02-17 OHEPEE, Ravenshaw University, Cuttack |
| Contributed Indexing: | Keywords: apocarotenoid synthesis; gene ontology; molecular modelling; networks; pathways; proteomics; saffron flower |
| Substance Nomenclature: | 0 (Plant Proteins) 36-88-4 (Carotenoids) 0 (Terpenes) 0 (Proteome) |
| Entry Date(s): | Date Created: 20260530 Date Completed: 20260926 Latest Revision: 20260926 |
| Update Code: | 20260927 |
| DOI: | 10.1002/pmic.70151 |
| PMID: | 42216577 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 1615-9861 |
|---|---|
| DOI: | 10.1002/pmic.70151 |