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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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Wang Z, Zhang L, Dong C, Guo J, Jin L, Wei P, Li F, Zhang X, Wang R. Characterization and functional analysis of phytoene synthase gene family in tobacco. BMC PLANT BIOLOGY 2021; 21:32. [PMID: 33413114 PMCID: PMC7791662 DOI: 10.1186/s12870-020-02816-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/22/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Carotenoids play important roles in photosynthesis, hormone signaling, and secondary metabolism. Phytoene synthase (PSY) catalyzes the first step of the carotenoid biosynthetic pathway. In this study, we aimed to characterize the PSY genes in tobacco and analyze their function. RESULTS In this study, we identified three groups of PSY genes, namely PSY1, PSY2, and PSY3, in four Nicotiana species; phylogenetic analysis indicated that these genes shared a high similarity with those in tomato but not with those in monocots such as rice and maize. The expression levels of PSY1 and PSY2 were observed to be highest in leaves compared to other tissues, and they could be elevated by treatment with certain phytohormones and exposure to strong light. No PSY3 expression was detected under these conditions. We constructed virus-induced PSY1 and PSY2 silencing in tobacco and found that the newly emerged leaves in these plants were characterized by severe bleaching and markedly decreased carotenoid and chlorophyll content. Thylakoid membrane protein complex levels in the gene-silenced plants were also less than those in the control plants. The chlorophyll fluorescence parameters such as Fv/Fm, ΦPSII, qP, and NPQ, which reflect photosynthetic system activities, of the gene-silenced plants were also significantly decreased. We further performed RNA-Seq and metabonomics analysis between gene-silenced tobacco and control plants. RNA-Seq results showed that abiotic stress, isoprenoid compounds, and amino acid catabolic processes were upregulated, whereas the biosynthesis of cell wall components was downregulated. Metabolic analysis results were consistent with the RNA-Seq. We also found the downstream genes in carotenoid biosynthesis pathways were upregulated, and putative transcription factors that regulate carotenoid biosynthesis were identified. CONCLUSIONS Our results suggest that PSY can regulate carotenoid contents not only by controlling the first biosynthesis step but also by exerting effects on the expression of downstream genes, which would thereby affect photosynthetic activity. Meanwhile, PSY may affect other processes such as amino acid catabolism and cell wall organization. The information we report here may aid further research on PSY genes and carotenoid biosynthesis.
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Affiliation(s)
- Zhaojun Wang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lin Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
- China Tobacco Yunnan Industrial Co., Ltd., Kunming, 650231, Yunnan, China
| | - Chen Dong
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jinggong Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Lifeng Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pan Wei
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Xiaoquan Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Ran Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
- School of Life Sciences, School of Agricultural Sciences, Zhengzhou University, No. 100 Science Road, Gaoxin Distract, Zhengzhou, 450001, Henan, China.
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Mortimer CL, Misawa N, Perez-Fons L, Robertson FP, Harada H, Bramley PM, Fraser PD. The Formation and Sequestration of Nonendogenous Ketocarotenoids in Transgenic Nicotiana glauca. PLANT PHYSIOLOGY 2017; 173:1617-1635. [PMID: 28153925 PMCID: PMC5338661 DOI: 10.1104/pp.16.01297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/18/2017] [Indexed: 05/02/2023]
Abstract
Ketolated and hydroxylated carotenoids are high-value compounds with industrial, food, and feed applications. Chemical synthesis is currently the production method of choice for these compounds, with no amenable plant sources readily available. In this study, the 4,4' β-oxygenase (crtW) and 3,3' β-hydroxylase (crtZ) genes from Brevundimonas sp. SD-212 were expressed under constitutive transcriptional control in Nicotiana glauca, which has an emerging potential as a biofuel and biorefining feedstock. The transgenic lines produced significant levels of nonendogenous carotenoids in all tissues. In leaf and flower, the carotenoids (∼0.5% dry weight) included 0.3% and 0.48%, respectively, of nonendogenous ketolated and hydroxylated carotenoids. These were 4-ketolutein, echinenone (and its 3-hydroxy derivatives), canthaxanthin, phoenicoxanthin, 4-ketozeaxanthin, and astaxanthin. Stable, homozygous genotypes expressing both transgenes inherited the chemotype. Subcellular fractionation of vegetative tissues and microscopic analysis revealed the presence of ketocarotenoids in thylakoid membranes, not predominantly in the photosynthetic complexes but in plastoglobules. Despite ketocarotenoid production and changes in cellular ultrastructure, intermediary metabolite levels were not dramatically affected. The study illustrates the utility of Brevundimonas sp. SD-212 CRTZ and CRTW to produce ketocarotenoids in a plant species that is being evaluated as a biorefining feedstock, the adaptation of the plastid to sequester nonendogenous carotenoids, and the robustness of plant metabolism to these changes.
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Affiliation(s)
- Cara L Mortimer
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Norihiko Misawa
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Francesca P Robertson
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Hisashi Harada
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Peter M Bramley
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom (C.L.M., L.P.-F., F.P.R., P.M.B., P.D.F.); and
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan (N.M., H.H.)
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5
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Drapal M, Wheeler PR, Fraser PD. Metabolite analysis of Mycobacterium species under aerobic and hypoxic conditions reveals common metabolic traits. MICROBIOLOGY-SGM 2016; 162:1456-1467. [PMID: 27312482 DOI: 10.1099/mic.0.000325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A metabolite profiling approach has been implemented to elucidate metabolic adaptation at set culture conditions in five Mycobacterium species (two fast- and three slow-growing) with the potential to act as model organisms for Mycobacterium tuberculosis (Mtb). Analysis has been performed over designated growth phases and under representative environments (nutrient and oxygen depletion) experienced by Mtb during infection. The procedure was useful in determining a range of metabolites (60-120 compounds) covering nucleotides, amino acids, organic acids, saccharides, fatty acids, glycerols, -esters, -phosphates and isoprenoids. Among these classes of compounds, key biomarker metabolites, which can act as indicators of pathway/process activity, were identified. In numerous cases, common metabolite traits were observed for all five species across the experimental conditions (e.g. uracil indicating DNA repair). Amino acid content, especially glutamic acid, highlighted the different properties between the fast- and slow-growing mycobacteria studied (e.g. nitrogen assimilation). The greatest similarities in metabolite composition between fast- and slow-growing mycobacteria were apparent under hypoxic conditions. A comparison to previously reported transcriptomic data revealed a strong correlation between changes in transcription and metabolite content. Collectively, these data validate the changes in the transcription at the metabolite level, suggesting transcription exists as one of the predominant modes of cellular regulation in Mycobacterium. Sectors with restricted correlation between metabolites and transcription (e.g. hypoxic cultivation) warrant further study to elucidate and exploit post-transcriptional modes of regulation. The strong correlation between the laboratory conditions used and data derived from in vivo conditions, indicate that the approach applied is a valuable addition to our understanding of cell regulation in these Mycobacterium species.
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Affiliation(s)
- Margit Drapal
- School of Biological Sciences, Royal Holloway University of London, Egham, UK
| | - Paul R Wheeler
- Tuberculosis Research Group, Veterinary Laboratories Agency Weybridge, New Haw, UK
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham, UK
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6
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Meléndez-Martínez AJ, Mapelli-Brahm P, Benítez-González A, Stinco CM. A comprehensive review on the colorless carotenoids phytoene and phytofluene. Arch Biochem Biophys 2015; 572:188-200. [DOI: 10.1016/j.abb.2015.01.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/30/2014] [Accepted: 01/04/2015] [Indexed: 12/22/2022]
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7
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Zhang F, Wang Z, Dong W, Sun C, Wang H, Song A, He L, Fang W, Chen F, Teng N. Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding. Sci Rep 2014; 4:6536. [PMID: 25288482 PMCID: PMC4187010 DOI: 10.1038/srep06536] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/26/2014] [Indexed: 12/25/2022] Open
Abstract
Embryo abortion is the main cause of failure in chrysanthemum cross breeding, and the genes and proteins associated with embryo abortion are poorly understood. Here, we applied RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic profiles of normal and abortive embryos. More than 68,000 annotated unigenes and 700 proteins were obtained from normal and abortive embryos. Functional analysis showed that 140 differentially expressed genes (DEGs) and 41 differentially expressed proteins (DEPs) were involved in embryo abortion. Most DEGs and DEPs associated with cell death, protein degradation, reactive oxygen species scavenging, and stress-response transcriptional factors were significantly up-regulated in abortive embryos relative to normal embryos. In contrast, most genes and proteins related to cell division and expansion, the cytoskeleton, protein synthesis and energy metabolism were significantly down-regulated in abortive embryos. Furthermore, abortive embryos had the highest activity of three executioner caspase-like enzymes. These results indicate that embryo abortion may be related to programmed cell death and the senescence- or death-associated genes or proteins contribute to embryo abortion. This adds to our understanding of embryo abortion and will aid in the cross breeding of chrysanthemum and other crops in the future.
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Affiliation(s)
- Fengjiao Zhang
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Zhiquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Dong
- China Rural Technology Development Center, Beijing 100045, China
| | - Chunqing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lizhong He
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fadi Chen
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
| | - Nianjun Teng
- 1] College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China [2] Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology &Equipment, Nanjing 210095, China
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8
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Juarez P, Fernandez-del-Carmen A, Rambla JL, Presa S, Mico A, Granell A, Orzaez D. Evaluation of unintended effects in the composition of tomatoes expressing a human immunoglobulin A against rotavirus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:8158-8168. [PMID: 25065456 DOI: 10.1021/jf502292g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The production of neutralizing immunoglobulin A (IgA) in edible fruits as a means of oral passive immunization is a promising strategy for the inexpensive treatment of mucosal diseases. This approach is based on the assumption that the edible status remains unaltered in the immunoglobulin-expressing fruit, and therefore extensive purification is not required for mucosal delivery. However, unintended effects associated with IgA expression such as toxic secondary metabolites and protein allergens cannot be dismissed a priori and need to be investigated. This paper describes a collection of independent transgenic tomato lines expressing a neutralizing human IgA against rotavirus, a mucosal pathogen producing severe diarrhea episodes. This collection was used to evaluate possible unintended effects associated with recombinant IgA expression. A comparative analysis of protein and secondary metabolite profiles using wild type lines and other commercial varieties failed to find unsafe features significantly associated with IgA expression. Preliminary, the data indicate that formulations derived from IgA tomatoes are as safe for consumption as equivalent formulations derived from wild type tomatoes.
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MESH Headings
- Allergens/adverse effects
- Allergens/genetics
- Allergens/metabolism
- Antibodies, Neutralizing/adverse effects
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/metabolism
- Dietary Proteins/adverse effects
- Dietary Proteins/metabolism
- Food, Genetically Modified/adverse effects
- Fruit/adverse effects
- Fruit/chemistry
- Fruit/genetics
- Fruit/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Humans
- Immunization, Passive/adverse effects
- Immunoglobulin A/adverse effects
- Immunoglobulin A/genetics
- Immunoglobulin A/metabolism
- Least-Squares Analysis
- Solanum lycopersicum/adverse effects
- Solanum lycopersicum/chemistry
- Solanum lycopersicum/genetics
- Solanum lycopersicum/metabolism
- Plant Proteins/adverse effects
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/adverse effects
- Plants, Genetically Modified/chemistry
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Principal Component Analysis
- Recombinant Proteins/adverse effects
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Rotavirus/growth & development
- Rotavirus/immunology
- Rotavirus Infections/immunology
- Rotavirus Infections/prevention & control
- Rotavirus Infections/virology
- Secondary Metabolism
- Spain
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Affiliation(s)
- Paloma Juarez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientı́ficas, Universidad Politécnica de Valencia , Camino de Vera s/n, 46022 Valencia, Spain
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Mora L, Bramley PM, Fraser PD. Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit. Proteomics 2014; 13:2016-30. [PMID: 23616442 DOI: 10.1002/pmic.201200480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/01/2013] [Accepted: 04/10/2013] [Indexed: 01/01/2023]
Abstract
A key global challenge for plant biotechnology is addressing food security, whereby provision must be made to feed 9 billion people with nutritional feedstuffs by 2050. To achieve this step change in agricultural production new crop varieties are required that are tolerant to environmental stresses imposed by climate change, have better yields, are more nutritious and require less resource input. Genetic modification (GM) and marker-assisted screening will need to be fully utilised to deliver these new crop varieties. To evaluate these varieties both in terms of environmental and food safety and the rational design of traits a systems level characterisation is necessary. To link the transcriptome to the metabolome, quantitative proteomics is required. Routine quantitative proteomics is an important challenge. Gel-based densitometry and MS analysis after stable isotope labeling have been employed. In the present article, we describe the application of a label-free approach that can be used in combination with SDS-PAGE and reverse-phase chromatography to evaluate the changes in the proteome of new crop varieties. The workflow has been optimised for protein coverage, accuracy and robustness, then its application demonstrated using a GM tomato variety engineered to deliver nutrient dense fruit.
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Affiliation(s)
- Leticia Mora
- Centre for Systems and Synthetic Biology, School of Biological Sciences, Royal Holloway, University of London, Egham, UK
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10
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Nogueira M, Mora L, Enfissi EM, Bramley PM, Fraser PD. Subchromoplast sequestration of carotenoids affects regulatory mechanisms in tomato lines expressing different carotenoid gene combinations. THE PLANT CELL 2013; 25:4560-79. [PMID: 24249831 PMCID: PMC3875736 DOI: 10.1105/tpc.113.116210] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/07/2013] [Accepted: 10/15/2013] [Indexed: 05/18/2023]
Abstract
Metabolic engineering of the carotenoid pathway in recent years has successfully enhanced the carotenoid contents of crop plants. It is now clear that only increasing biosynthesis is restrictive, as mechanisms to sequestrate these increased levels in the cell or organelle should be exploited. In this study, biosynthetic pathway genes were overexpressed in tomato (Solanum lycopersicum) lines and the effects on carotenoid formation and sequestration revealed. The bacterial Crt carotenogenic genes, independently or in combination, and their zygosity affect the production of carotenoids. Transcription of the pathway genes was perturbed, whereby the tissue specificity of transcripts was altered. Changes in the steady state levels of metabolites in unrelated sectors of metabolism were found. Of particular interest was a concurrent increase of the plastid-localized lipid monogalactodiacylglycerol with carotenoids along with membranous subcellular structures. The carotenoids, proteins, and lipids in the subchromoplast fractions of the transgenic tomato fruit with increased carotenoid content suggest that cellular structures can adapt to facilitate the sequestration of the newly formed products. Moreover, phytoene, the precursor of the pathway, was identified in the plastoglobule, whereas the biosynthetic enzymes were in the membranes. The implications of these findings with respect to novel pathway regulation mechanisms are discussed.
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Chan Z. Proteomic responses of fruits to environmental stresses. FRONTIERS IN PLANT SCIENCE 2013; 3:311. [PMID: 23335934 PMCID: PMC3541545 DOI: 10.3389/fpls.2012.00311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/24/2012] [Indexed: 05/18/2023]
Abstract
Fruits and vegetables are extremely susceptible to decay and easily lose commercial value after harvest. Different strategies have been developed to control postharvest decay and prevent quality deterioration during postharvest storage, including cold storage, controlled atmosphere (CA), and application of biotic and abiotic stimulus. In this review, mechanisms related to protein level responses of host side and pathogen side were characterized. Protein extraction protocols have been successfully developed for recalcitrant, low protein content fruit tissues. Comparative proteome profiling and functional analysis revealed that defense related proteins, energy metabolism, and antioxidant pathway played important roles in fruits in response to storage conditions and exogenous elicitor treatments. Secretome of pathogenic fungi has been well-investigated and the results indicated that hydrolytic enzymes were the key virulent factors for the pathogen infection. These protein level changes shed new light on interaction among fruits, pathogens, and environmental conditions. Potential postharvest strategies to reduce risk of fruit decay were further proposed based on currently available proteomic data.
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
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12
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Ricroch AE. Assessment of GE food safety using '-omics' techniques and long-term animal feeding studies. N Biotechnol 2012; 30:349-54. [PMID: 23253614 DOI: 10.1016/j.nbt.2012.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 11/29/2012] [Accepted: 12/03/2012] [Indexed: 12/28/2022]
Abstract
Despite the fact that a thorough, lengthy and costly evaluation of genetically engineered (GE) crop plants (including compositional analysis and toxicological tests) is imposed before marketing some European citizens remain sceptical of the safety of GE food and feed. In this context, are additional tests necessary? If so, what can we learn from them? To address these questions, we examined data from 60 recent high-throughput '-omics' comparisons between GE and non-GE crop lines and 17 recent long-term animal feeding studies (longer than the classical 90-day subchronic toxicological tests), as well as 16 multigenerational studies on animals. The '-omics' comparisons revealed that the genetic modification has less impact on plant gene expression and composition than that of conventional plant breeding. Moreover, environmental factors (such as field location, sampling time, or agricultural practices) have a greater impact than transgenesis. None of these '-omics' profiling studies has raised new safety concerns about GE varieties; neither did the long-term and multigenerational studies on animals. Therefore, there is no need to perform such long-term studies in a case-by-case approach, unless reasonable doubt still exists after conducting a 90-day feeding test. In addition, plant compositional analysis and '-omics' profiling do not indicate that toxicological tests should be mandatory. We discuss what complementary fundamental studies should be performed and how to choose the most efficient experimental design to assess risks associated with new GE traits. The possible need to update the current regulatory framework is discussed.
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Affiliation(s)
- Agnès E Ricroch
- AgroParisTech, Chair of Evolutionary Genetics and Plant Breeding, 16, rue Claude-Bernard, 75005 Paris, France.
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