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Chin CF, Tan HS. The Use of Proteomic Tools to Address Challenges Faced in Clonal Propagation of Tropical Crops through Somatic Embryogenesis. Proteomes 2018; 6:proteomes6020021. [PMID: 29734680 PMCID: PMC6027288 DOI: 10.3390/proteomes6020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 12/16/2022] Open
Abstract
In many tropical countries with agriculture as the mainstay of the economy, tropical crops are commonly cultivated at the plantation scale. The successful establishment of crop plantations depends on the availability of a large quantity of elite seedling plants. Many plantation companies establish plant tissue culture laboratories to supply planting materials for their plantations and one of the most common applications of plant tissue culture is the mass propagation of true-to-type elite seedlings. However, problems encountered in tissue culture technology prevent its applications being widely adopted. Proteomics can be a powerful tool for use in the analysis of cultures, and to understand the biological processes that takes place at the cellular and molecular levels in order to address these problems. This mini review presents the tissue culture technologies commonly used in the propagation of tropical crops. It provides an outline of some the genes and proteins isolated that are associated with somatic embryogenesis and the use of proteomic technology in analysing tissue culture samples and processes in tropical crops.
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Affiliation(s)
- Chiew Foan Chin
- School of Biosciences, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Hooi Sin Tan
- School of Biosciences, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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Xu Z, Zhang C, Zhang X, Liu C, Wu Z, Yang Z, Zhou K, Yang X, Li F. Transcriptome profiling reveals auxin and cytokinin regulating somatic embryogenesis in different sister lines of cotton cultivar CCRI24. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:631-42. [PMID: 23710882 DOI: 10.1111/jipb.12073] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/15/2013] [Indexed: 05/22/2023]
Abstract
To get a broader view on the molecular mechanisms underlying somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.), global analysis of cotton transcriptome dynamics during SE in different sister lines was performed using RNA-Seq. A total of 204 349 unigenes were detected by de novo assembly of the 214 977 462 Illumina reads. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) measurements were positively correlated with the RNA-Seq results for almost all the tested genes (R(2) = 0.841, correlation was significant at the 0.01 level). Different phytohormone (auxin and cytokinin) concentration ratios in medium and the endogenous content changes of these two phytohormones at two stages in different sister lines suggested the roles of auxin and cytokinin during cotton SE. On the basis of global gene regulation of phytohormone-related genes, numerous genes from all the differentially expressed transcripts were involved in auxin and cytokinin biosynthesis and signal transduction pathways. Analyses of differentially expressed genes that were involved in these pathways revealed the substantial changes in gene type and abundance between two sister lines. Isolation, cloning and silencing/overexpressing the genes that revealed remarkable up- or down-expression during cotton SE were important. Furthermore, auxin and cytokinin play a primary role in SE, but potential cross-talk with each other or other factors remains unclear.
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Affiliation(s)
- Zhenzhen Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences, Anyang, 455000, China
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Jellouli N, Salem AB, Ghorbel A, Jouira HB. Evaluation of protein extraction methods for Vitis vinifera leaf and root proteome analysis by two-dimensional electrophoresis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:933-40. [PMID: 20883445 DOI: 10.1111/j.1744-7909.2010.00973.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An efficient protein extraction method is crucial to ensure successful separation by two-dimensional electrophoresis (2-DE) for recalcitrant plant species, in particular for grapevine (Vitis vinifera L.). Trichloroacetic acid-acetone (TCA-acetone) and phenol extraction methods were evaluated for proteome analysis of leaves and roots from the Tunisian cultivar 'Razegui'. The phenol-based protocol proved to give a higher protein yield, a greater spot resolution, and a minimal streaking on 2-DE gels for both leaf and root tissues compared with the TCA-based protocol. Furthermore, the highest numbers of detected proteins on 2-DE gels were observed using the phenol extraction from leaves and roots as compared with TCA-acetone extraction.
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Yang X, Zhang X. Regulation of Somatic Embryogenesis in Higher Plants. CRITICAL REVIEWS IN PLANT SCIENCES 2010; 29:36-57. [PMID: 0 DOI: 10.1080/07352680903436291] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Xiyan Yang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
| | - Xianlong Zhang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
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Marsoni M, Bracale M, Espen L, Prinsi B, Negri AS, Vannini C. Proteomic analysis of somatic embryogenesis in Vitis vinifera. PLANT CELL REPORTS 2008; 27:347-56. [PMID: 17874111 DOI: 10.1007/s00299-007-0438-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/23/2007] [Accepted: 08/15/2007] [Indexed: 05/17/2023]
Abstract
Two dimensional gel electrophoresis coupled to mass spectrometry has been used to study the somatic embryogenesis in Vitis vinifera, by comparing embryogenic and non embryogenic calluses of the Thompson seedless cv. More than 1,000 spots were reproducibly resolved in colloidal Coomassie brilliant blue stained gels over a pI nonlinear range of 3-10 in the first dimension and using homogeneous 12.5% polyacrylamide gels in the second dimension. The expression pattern of 35 spots differed significantly between the two samples. These spots were processed by mass spectrometry analysis and the protein identity was assigned by using both the non-redundant protein and EST databases. Several responsive proteins, some already known to be involved in the somatic embryogenesis process while others, for the first time put into relation with this process, have been described. Moreover, they have been subdivided in functional categories, and their putative role is discussed in terms of their relevance in the somatic embryogenesis process.
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Affiliation(s)
- Milena Marsoni
- Dipartimento Ambiente-Salute-Sicurezza, Università dell'Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
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Zeng F, Zhang X, Cheng L, Hu L, Zhu L, Cao J, Guo X. A draft gene regulatory network for cellular totipotency reprogramming during plant somatic embryogenesis. Genomics 2007; 90:620-8. [PMID: 17884330 DOI: 10.1016/j.ygeno.2007.07.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 06/23/2007] [Accepted: 07/17/2007] [Indexed: 10/22/2022]
Abstract
The complexity of the somatic embryogenesis (SE) transcriptome suggests that numerous molecules are involved. To understand better the functional genomics of complex molecular systems during this important reprogramming process, we used bioinformatics and a pathway database to construct a draft network based on transcriptionally regulated SE-related genes, from functional genomics assays readout to high-level biological data interpretation. Here, a complex molecular system was unraveled by this network. This draft network is a potential reservoir for hundreds of testable predictions about cellular processes in early SE. This work could provide a useful test for modeling of a systems network and may have merit as a study presenting an advanced technology application due to its biological and economical importance. The approach presented here is scalable and can be extended to include additional data types. In particular, this effective system approach will be applied to various targeted gene networks in the future.
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Affiliation(s)
- Fanchang Zeng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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Vincent D, Wheatley MD, Cramer GR. Optimization of protein extraction and solubilization for mature grape berry clusters. Electrophoresis 2006; 27:1853-65. [PMID: 16586412 DOI: 10.1002/elps.200500698] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein extraction from grape berries has been challenging, particularly in mature berries, which can have sugar concentrations as high as 26%. Grape skins and seeds contain large amounts of polyphenols, which can also interfere with efficient protein extraction. In plants, two extraction protocols, TCA/acetone-based and phenol-based methods, have been mainly used to extract proteins from different organs or tissues on many species. However, few results have been reported for grape berry clusters. We wanted to determine which of these protocols was optimal for berry clusters in order to achieve both efficient protein extraction and high spot resolution on 2-D gels. Four protocols, derived from either TCA/acetone or phenol procedures, were tested on mature Cabernet Sauvignon whole berry clusters. The phenol-based protocols were superior to the TCA/acetone methods, showing larger protein yields and greater spot resolution on 2-D gels. One method was clearly superior to the rest, a phenol-based extraction method combined with resuspension in the presence of both urea and thiourea as chaotropes. A total of 81 spots were excised and identified following MALDI-TOF/TOF MS analyses. Their identification helped further characterize the specificity of each extraction procedure.
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Affiliation(s)
- Delphine Vincent
- Department of Biochemistry, University of Nevada, Reno, NV 89557, USA
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Ruebelt MC, Lipp M, Reynolds TL, Astwood JD, Engel KH, Jany KD. Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of genetically modified crops. 2. Assessing natural variability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:2162-8. [PMID: 16536591 DOI: 10.1021/jf052357y] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteomics is currently tested as a complementary tool for the safety assessment of genetically modified (GM) crops. Understanding the natural variability of the proteome is crucial for the interpretation of biological differences between transgenic and nontransgenic parental lines. The natural variation of seed protein profiles among a set of 12 Arabidopsis thaliana ecotypes was determined by utilizing two-dimensional electrophoresis (2DE). The total number of different resolved protein spots found among the 12 ecotypes was 931 with a range of 573 (Mt-0) to 653 (Condara) in any one ecotype. Although the ecotypes were grown side-by-side in an environmentally controlled growth chamber, almost half of the resolved spots varied with respect to their presence/absence, and 95% of the spots present in all ecotypes varied in spot quantity (2-53-fold). In the evaluation of unintended effects of genetic modification, it is concluded that the experimental design must account for existing natural variability, which, in the case of the expressed proteome, can be substantial.
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Affiliation(s)
- Martin C Ruebelt
- Product Safety Center, Monsanto Company, 800 North Lindbergh Boulevard, St. Louis, Missouri 63167, USA.
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Imin N, Nizamidin M, Daniher D, Nolan KE, Rose RJ, Rolfe BG. Proteomic analysis of somatic embryogenesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treatments. PLANT PHYSIOLOGY 2005; 137:1250-60. [PMID: 15749990 PMCID: PMC1088318 DOI: 10.1104/pp.104.055277] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 01/06/2005] [Accepted: 01/09/2005] [Indexed: 05/18/2023]
Abstract
The Medicago truncatula line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than wild-type Jemalong. We have compared proteomes of tissue cultures from leaf explants of these two lines. Both 2HA and Jemalong explants were grown on media containing the auxin 1-naphthaleneacetic acid and the cytokinin 6-benzylaminopurine. Proteins were extracted from the cultures at different time points (2, 5, and 8 weeks), separated by two-dimensional gel electrophoresis, and detected by silver staining. More than 2,000 proteins could be reproducibly resolved and detected on each gel. Statistical analysis showed that 54 protein spots were significantly (P < 0.05) changed in expression (accumulation) during the 8 weeks of culture, and most of these spots were extracted from colloidal Coomassie-stained two-dimensional gel electrophoresis gels and were subjected to matrix-assisted laser desorption ionization time-of-flight mass spectrometry or liquid chromatography-tandem mass spectrometry analysis. Using a publicly available expressed sequence tag database and the Mascot search engine, we were able to identify 16 differentially expressed proteins. More than 60% of the differentially expressed protein spots had very different patterns of gene expression between 2HA and Jemalong during the 8 weeks of culture.
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Affiliation(s)
- Nijat Imin
- Australian Research Council Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra City, Australian Capital Territory, 2601, Australia
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Bertoldi D, Tassoni A, Martinelli L, Bagni N. Polyamines and somatic embryogenesis in two Vitis vinifera cultivars. PHYSIOLOGIA PLANTARUM 2004; 120:657-666. [PMID: 15032828 DOI: 10.1111/j.0031-9317.2004.0282.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Polyamine content and activities of enzymes of polyamine biosynthesis were assayed during somatic embryogenesis in Vitis vinifera callus cultures of Chardonnay and Brachetto 'a grappolo lungo' (Brachetto g.l.) cultivars. The analyses were carried out on embryogenic callus samples, embryos at different stages and developing plants. Polyamine content, both in the free and PCA-soluble conjugated form, was higher in Brachetto g.l. than in Chardonnay, and putrescine was present at higher concentrations than the other polyamines. In all samples of both cultivars, ornithine decarboxylase activity (ODC, EC 4.1.1.17) was higher than arginine decarboxylase (ADC, EC 4.1.1.19), with a maximum in developing plant roots. S-Adenosylmethionine decarboxylase (SAMDC, EC 4.1.1.50) activity displayed a similar trend. The activities of all three enzymes were detected both in the supernatant and pellet fractions, indicating for the first time the presence of SAMDC activity in the particulate fraction. Particularly in the Chardonnay cultivar, an increase in the mRNAs expression patterns of ODC and SAMDC during morphogenesis from small embryos to plantlets was detected by northern blot, suggesting a direct correlation with enzymatic activities.
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Affiliation(s)
- Daniela Bertoldi
- Department of Biology e.s. and Interdepartmental Centre for Biotechnology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
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Sallandrouze A, Faurobert M, El Maataoui M, Espagnac H. Two-dimensional electrophoretic analysis of proteins associated with somatic embryogenesis development in Cupressus sempervirens L. Electrophoresis 1999; 20:1109-19. [PMID: 10344292 DOI: 10.1002/(sici)1522-2683(19990101)20:4/5<1109::aid-elps1109>3.0.co;2-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two-dimensional gel electrophoretic analysis and histological studies were performed on somatic embryos in cypress. Embryogenic cultures were obtained from in vitro culture of immature seeds. On a modified Murashige and Skoog (MS) medium they showed an intense and repetitive cleavage polyembryogenesis phenomenon which maintained them in a continuous proliferating status instead of undergoing a complete embryogenic development. Only the addition of bovine serum albumin to the culture allowed somatic embryo development and maturation. Major histological differences were noticed between developing and nondeveloping embryogenic cultures. Attempts to find proteins that could be associated with developmental stages of somatic embryos have been achieved. Proteins were extracted and analyzed by two-dimensional electrophoresis from nondeveloping embryogenic cultures (S0) and from embryogenic cultures at three different stages of somatic embryo development: small size and rounded shape embryos (S1), increased size embryos with a well-developed suspensor (S2) and embryos with two well-separated cotyledons (S3). The results revealed some qualitative and quantitative protein variations between the two cultures. Some could be connected with the induction of pro-embryo differentiation whereas others should be more related to the mechanisms involved in somatic embryo development and maturation. Specific polypeptides associated with the presence of bovine serum albumin (BSA) in the medium have been detected.
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Affiliation(s)
- A Sallandrouze
- Département de Biologie, Université d'Avignon et des Pays du Vaucluse, Faculté des Sciences, France
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Martinelli L, Gianazza E. Biochemical changes during regeneration of sunflower (Helianthus annuus L.). Electrophoresis 1996; 17:191-7. [PMID: 8907539 DOI: 10.1002/elps.1150170131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The main developmental stages in Helianthus annuus organogenesis have been studied in the sunflower hybrid "Giove". Shoot regeneration was obtained with high efficiency from mature seed cotyledons. Two-dimensional electrophoresis of protein extracts as well as the isozyme patterns of acid phosphatase, alcohol dehydrogenase, esterase, gluconate-6-phosphate dehydrogenase and phosphoglucomutase were compared during growth, callusing and regeneration. Two-dimensional protein patterns were similar, although polypeptides specific for each developmental phase could be identified. Different 2,4-dichlorophenoxyacetic acid concentrations or the sampling of specific regions of the seed did not result in significant differences in protein patterns. The activity of alcohol dehydrogenase and phosphoglucomutase appeared very low. For gluconate-6-phosphate dehydrogenase no difference, related either to the genotype or to different morphological stages, could be observed; the expression of acid phosphatase varied in a nonsystematic fashion. The isozyme pattern of esterase was related to the genotype as well as to the morphogenic phase.
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Affiliation(s)
- L Martinelli
- Laboratorio Biotecnologie, Istituto Agrario, San Michele all'Adige, Italy
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