Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L.
Abstract
1. Introduction
2. Results and Discussion
2.1. Obtaining Two Developmental Stages of J. curcas Somatic Embryos in Liquid Medium
2.2. Two-Dimensional Proteome Analysis of Pre-Globular and Globular Somatic Embryos
2.3. Functional Classification of Proteins in Pre-Globular and Globular Somatic Embryos
2.3.1. Enhanced Metabolism and Cellular Activity at the Globular Stage
2.3.2. Photosynthetic Priming for Autotrophic Growth
2.3.3. Protein Folding and Degradation Mechanisms
2.3.4. Translational Regulation: Role of eIF3f
2.3.5. Auxin Signaling and Embryo Developmental Arrest
2.4. Gene Expression Analysis in J. curcas
3. Materials and Methods
3.1. Plant Material for Somatic Embryogenesis
3.2. Induction of Callus
3.3. Induction of Somatic Embryos in Liquid Medium
3.4. Protein Extraction
3.5. Two-Dimensional IEF/SDS–PAGE and Protein Staining
3.6. Image Acquisition and Analysis
3.7. In-Gel Digestion and Mass Spectrometry Analysis
3.8. Biological Function
3.9. RNA Extraction and cDNA Synthesis
3.10. Gene Expression Analysis via RT-qPCR
3.11. Statistical Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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ImageMasterTM 2D Platinum Data | QuickGo Data | ||||
---|---|---|---|---|---|
Spot Number a | Protein Number b | Fold Change c | Protein Name d | GO SLIM e | GO TERMS f |
21 | 1 | 4.02 | 14-3-3 protein 6 | __ | __ |
319 | 1 | 3.63 | Hypothetical protein JCGZ_08406 | __ | __ |
558 | 1 | 3.23 | Endo-1,3;1,4-beta-D-glucanase | __ | __ |
230 | 3 | 1.94 | Hypothetical protein JCGZ_19572 | __ | __ |
215 | 1 | 4.33 | Fructokinase-2 | Carbohydrate metabolic process | Fructose metabolic process; carbohydrate phosphorylation |
57 | 2 | 4.43 | Nucleoside diphosphate kinase | Nucleobase-containing compound metabolic process | GTP, UTP, CTP biosynthetic process |
52 | 1 | 1.74 | Proteasome subunit alpha type | Protein metabolic process | Ubiquitin-dependent protein catabolic process |
305 | 1 | 5.58 | Glutathione S-transferase PARB | Response to chemical stimulus | Glutathione metabolic process; response to toxic substance |
57 | 1 | 4.43 | Superoxide dismutase [Cu-Zn] | Response to stress and chemical stimulus | Superoxide metabolic process; removal of superoxide radicals; cellular oxidant detoxification |
239 | 1 | 3.64 | LysM domain receptor-like kinase 3 | Response to stress, biotic stimulus; external stimulus | Innate immune response |
404 | 1 | 2.92 | Eukaryotic translation initiation factor 3 subunit F | Translation | Formation of cytoplasmic translation initiation complex; cytoplasmic translational initiation |
ImageMasterTM 2D Platinum Data | QuickGo Data | ||||
---|---|---|---|---|---|
Spot Number a | Protein Number b | Fold Change c | Protein Name d | GO SLIM e | GO TERMS f |
921 | 1 | unique | PREDICTED: Secoisolariciresinol dehydrogenase-like | __ | __ |
1274 | 1 | unique | Actin-7 | __ | _ |
1227 | 1 | unique | LOW QUALITY PROTEIN: receptor-like protein kinase FERONIA | __ | _ |
1278 | 3 | 3.6 | Secoisolariciresinol dehydrogenase | __ | __ |
629 | 1 | 3.47 | PREDICTED: Secoisolariciresinol dehydrogenase-like | __ | __ |
362 | 2 | 2.07 | Plastid-lipid-associated protein, chloroplastic | __ | _ |
575 | 1 | 3.43 | Cysteine synthase | Biosynthetic process | Cysteine biosynthetic process from serine |
1150 | 1 | 2.85 | Acidic endochitinase | Carbohydrate metabolic process | Carbohydrate metabolic process |
307 | 1 | 2.55 | Sedoheptulose-1,7-bisphosphatase, chloroplastic | Carbohydrate metabolic process | Carbohydrate metabolic process |
422 | 1 | 3.44 | WEB family protein At5g55860 isoform X1 | Cellular component organization | Chloroplast avoidance movement; chloroplast accumulation movement |
782 | 1 | Unique | Cytochrome b6-f complex iron-sulfur subunit | Cellular process | Transmembrane transport |
793 | 1 | 6.18 | Cytochrome b6-f complex iron-sulfur subunit | Cellular process | Transmembrane transport |
266 | 3 | 3.7 | AtpB | Cellular process | ATP metabolic process |
1100 | 1 | Unique | PREDICTED: Malate dehydrogenase | Generation of precursor metabolites and energy | Malate metabolic process |
1008 | 1 | Unique | PREDICTED: NADH dehydrogenase | Generation of precursor metabolites and energy | ATP synthesis coupled electron transport |
432 | 1 | 8.51 | ATP synthase subunit beta | Generation of precursor metabolites and energy | ATP biosynthetic process; ATP metabolic process |
955 | 1 | 5.06 | PREDICTED: Enolase-like | Generation of precursor metabolites and energy | Glycolytic process |
1010 | 1 | 4.59 | PREDICTED: Enolase | Generation of precursor metabolites and energy | Glycolytic process |
1254 | 2 | 4.13 | Malate dehydrogenase | Generation of precursor metabolites and energy | Tricarboxylic acid cycle; malate metabolic process |
1254 | 1 | 4.13 | Fructose-bisphosphate aldolase | Generation of precursor metabolites and energy | Glycolytic process |
374 | 1 | 2.85 | Fructose-bisphosphate aldolase | Generation of precursor metabolites and energy | Glycolytic process |
175 | 1 | 2.18 | Probable ribose-5-phosphate isomerase 3, chloroplastic | Generation of precursor metabolites and energy | Pentose-phosphate shunt, non-oxidative branch |
440 | 1 | 1.73 | ATP synthase subunit beta | Generation of precursor metabolites and energy | ATP biosynthetic process; ATP metabolic process |
568 | 1 | 1.52 | PREDICTED: Malate dehydrogenase, chloroplastic | Generation of precursor metabolites and energy | Tricarboxylic acid cycle; malate metabolic process |
422 | 4 | 3.44 | Type I inositol polyphosphate 5-phosphatase 13 isoform X1 | Lipid metabolic process | Phosphatidylinositol dephosphorylation |
1026 | 1 | Unique | L-lactate dehydrogenase | Metabolic process | Lactate metabolic process; pyruvate metabolic process |
879 | 1 | 4.57 | L-lactate dehydrogenase | Metabolic process | Lactate metabolic process; pyruvate metabolic process |
713 | 2 | 2.22 | 3-isopropylmalate dehydratase small subunit 3 | Metabolic process | Oxoacid metabolic process |
1064 | 3 | 3.68 | 4-hydroxy-4-methyl-2-oxoglutarate aldolase | Nucleic acids metabolic process | Regulation of RNA metabolic process |
686 | 1 | 13.68 | PREDICTED: Chlorophyll a-b binding protein 8, Chloroplastic | Photosynthesis | Photosynthesis, light harvesting |
708 | 1 | 9.59 | PREDICTED: Oxygen-evolving enhancer protein 2, chloroplastic | Photosynthesis | Photosynthesis |
704 | 1 | 5.42 | PREDICTED: Chlorophyll a-b binding protein of LHCII (light harvesting complex II) type 1 | Photosynthesis | Photosynthesis, light harvesting |
626 | 1 | 4.7 | PREDICTED: Oxygen-evolving enhancer protein 1, chloroplastic | Photosynthesis | Photosystem II assembly |
422 | 5 | 3.44 | Chlorophyll a-b binding protein 8, chloroplastic | Photosynthesis | Photosynthesis, light harvesting |
622 | 1 | 2.74 | PREDICTED: Oxygen-evolving enhancer protein 1, chloroplastic | Photosynthesis | Photosystem II assembly |
402 | 2 | unique | PREDICTED: Ubiquitin domain-containing protein DSK2a-like | Protein metabolic process | Ubiquitin-dependent protein catabolic process |
1278 | 2 | 3.6 | Proteasome subunit alpha type | Protein metabolic process | Ubiquitin-dependent protein catabolic process |
1278 | 1 | 3.6 | Proteasome subunit alpha type | Protein metabolic process | Ubiquitin-dependent protein catabolic process |
1130 | 1 | 3.11 | PREDICTED: Low-temperature-induced cysteine proteinase-like | Protein metabolic process | Proteolysis |
1130 | 2 | 3.11 | Proteasome subunit alpha type | Protein metabolic process | Proteasome-mediated ubiquitin-dependent protein catabolic process |
402 | 1 | unique | Protein disulfide-isomerase | Protein metabolic process; response to stress | Protein folding; response to endoplasmic reticulum stress |
480 | 1 | 4.4 | Alcohol dehydrogenase | Response to chemical stimulus | Formaldehyde catabolic process |
713 | 1 | 2.22 | Glutathione peroxidase | Response to stress and chemical stimulus | Response to oxidative stress |
1064 | 1 | 3.68 | Major allergen Pru ar 1 | Response to stress, chemical stimulus, endogenous stimulus; signal transduction | Defense response; abscisic acid-activated signaling pathway |
816 | 1 | 5.44 | Major allergen Pru ar 1-like | Response to stress and chemical stimulus, endogenous stimulus; signal transduction | Defense response; abscisic acid-activated signaling pathway; negative regulation of phosphoprotein phosphatase activity |
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Medina-Hernández, A.E.; Vera-Reyes, I.; Ríos-Castro, E.; Torres-Ruiz, J.J.; Ponce-Noyola, T.; Trejo-Tapia, G.; Garay-Arroyo, A.; Barrera-Cortés, J.; Ramos-Valdivia, A.C. Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L. Int. J. Mol. Sci. 2025, 26, 6384. https://doi.org/10.3390/ijms26136384
Medina-Hernández AE, Vera-Reyes I, Ríos-Castro E, Torres-Ruiz JJ, Ponce-Noyola T, Trejo-Tapia G, Garay-Arroyo A, Barrera-Cortés J, Ramos-Valdivia AC. Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L. International Journal of Molecular Sciences. 2025; 26(13):6384. https://doi.org/10.3390/ijms26136384
Chicago/Turabian StyleMedina-Hernández, Anamarel Edzná, Ileana Vera-Reyes, Emmanuel Ríos-Castro, Juan José Torres-Ruiz, Teresa Ponce-Noyola, Gabriela Trejo-Tapia, Adriana Garay-Arroyo, Josefina Barrera-Cortés, and Ana C. Ramos-Valdivia. 2025. "Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L." International Journal of Molecular Sciences 26, no. 13: 6384. https://doi.org/10.3390/ijms26136384
APA StyleMedina-Hernández, A. E., Vera-Reyes, I., Ríos-Castro, E., Torres-Ruiz, J. J., Ponce-Noyola, T., Trejo-Tapia, G., Garay-Arroyo, A., Barrera-Cortés, J., & Ramos-Valdivia, A. C. (2025). Proteomic Analysis and Expression of Selected Genes During the Early Somatic Embryogenesis of Jatropha curcas L. International Journal of Molecular Sciences, 26(13), 6384. https://doi.org/10.3390/ijms26136384