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Guan ZJ, Zheng M, Tang ZX, Wei W, Stewart CN. Proteomic Analysis of Bt cry1Ac Transgenic Oilseed Rape ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2319. [PMID: 37375944 DOI: 10.3390/plants12122319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Oilseed rape (Brassica napus L.) is an important cash crop, but transgenic oilseed rape has not been grown on a commercial scale in China. It is necessary to analyze the characteristics of transgenic oilseed rape before commercial cultivation. In our study, differential expression of total protein from the leaves in two transgenic lines of oilseed rape expressing foreign Bt Cry1Ac insecticidal toxin and their non-transgenic parent plant was analyzed using a proteomic approach. Only shared changes in both of the two transgenic lines were calculated. Fourteen differential protein spots were analyzed and identified, namely, eleven upregulated expressed protein spots and three downregulated protein spots. These proteins are involved in photosynthesis, transporter function, metabolism, protein synthesis, and cell growth and differentiation. The changes of these protein spots in transgenic oilseed rape may be attributable to the insertion of the foreign transgenes. However, the transgenic manipulation might not necessarily cause significant change in proteomes of the oilseed rape.
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Affiliation(s)
- Zheng-Jun Guan
- Department of Life Sciences, Yuncheng University, Yuncheng 044000, China
- State Key Laboratory of Vegetation and Climate Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Min Zheng
- State Key Laboratory of Vegetation and Climate Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Department of Hotel Management, Linyi Technician Institute, Linyi 276005, China
| | - Zhi-Xi Tang
- State Key Laboratory of Vegetation and Climate Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Wei
- State Key Laboratory of Vegetation and Climate Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - C Neal Stewart
- Department of Plant Sciences and Center for Agricultural Synthetic Biology, University of Tennessee, 2505 EJ Chapman Drive, Knoxville, TN 37996-4561, USA
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Ren Z, Qin L, Chen L, Xu H, Liu H, Guo H, Li J, Yang C, Hu H, Wu R, Zhou Y, Xue K, Liu B, Wang X. Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37318082 DOI: 10.1021/acs.jafc.3c01377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.
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Affiliation(s)
- Zhentao Ren
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Liang Qin
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Lulu Chen
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hualei Xu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Haiqiang Liu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hua Guo
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Jinrong Li
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Chenyu Yang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Hao Hu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Ran Wu
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Yijun Zhou
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Kun Xue
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Xiaodong Wang
- College of Life and Environmental Sciences, Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), State Ethnic Affairs Commission, Beijing 100081, China
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Platani M, Sokefun O, Bassil E, Apidianakis Y. Genetic engineering and genome editing in plants, animals and humans: Facts and myths. Gene 2023; 856:147141. [PMID: 36574935 DOI: 10.1016/j.gene.2022.147141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.
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Affiliation(s)
- Maria Platani
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Owolabi Sokefun
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Elias Bassil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
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Zhang X, Ding Y, Ma Q, Li F, Tao R, Li T, Zhu M, Ding J, Li C, Guo W, Zhu X. Comparative transcriptomic and metabolomic analysis revealed molecular mechanism of two wheat near-isogenic lines response to nitrogen application. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:47-57. [PMID: 36599275 DOI: 10.1016/j.plaphy.2022.12.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/13/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) is an essential nutrient element required for plant growth, and the development of wheat varieties with high nitrogen use efficiency (NUE) is an urgent need for sustainable crop production. However, the molecular mechanism of NUE between diverse wheat varieties in response to N application remains unclear. To reveal the possible molecular mechanisms underlying this complex phenomenon, we investigated the transcriptional and metabolic changes of flag leaves of two wheat near-isogenic lines (NILs) differing in NUE under two N fertilizer treatments. Comparative transcriptome analysis indicated that the expression levels of the genes responsible for carbon and nitrogen metabolism were significantly higher in high-NUE wheat. The metabolome comparison revealed that the activity of the tricarboxylic acid (TCA) cycle was enhanced in high-NUE wheat, while reduced in low-NUE wheat after the N fertilizer application. Additionally, amino acid metabolism increased in both wheat NILs but more increased in high-NUE wheat. In summary, more upregulated transcripts and metabolites were identified in high-NUE wheat, and this study provides valuable new insights for improving NUE in wheat.
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Affiliation(s)
- Xinbo Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Xuzhou Vocational College of Bioengineering, Xuzhou, 221006, China.
| | - Yonggang Ding
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Quan Ma
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Fujian Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Rongrong Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Tao Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
| | - Min Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Jinfeng Ding
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Chunyan Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Wenshan Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Xinkai Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Sun Y, Zhao H, Chen Z, Chen H, Li B, Wang C, Lin X, Cai Y, Zhou D, Ouyang L, Zhu C, He H, Peng X. Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:156. [PMID: 36616286 PMCID: PMC9824520 DOI: 10.3390/plants12010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huan Zhao
- Jiangxi Biotech Vocational College, JAU, Nanchang 330200, China
| | - Zhongkai Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Bai Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Chunlei Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
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Liu W, Meng L, Zhao W, Wang Z, Miao C, Wan Y, Jin W. Proteomic and Metabolomic Evaluation of Insect- and Herbicide-Resistant Maize Seeds. Metabolites 2022; 12:1078. [PMID: 36355161 PMCID: PMC9696663 DOI: 10.3390/metabo12111078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 05/27/2024] Open
Abstract
Label-free quantitative proteomic (LFQ) and widely targeted metabolomic analyses were applied in the safety evaluation of three genetically modified (GM) maize varieties, BBL, BFL-1, and BFL-2, in addition to their corresponding non-GM parent maize. A total of 76, 40, and 25 differentially expressed proteins (DEPs) were screened out in BBL, BFL-1, and BFL-2, respectively, and their abundance compared was with that in their non-GM parents. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most of the DEPs participate in biosynthesis of secondary metabolites, biosynthesis of amino acids, and metabolic pathways. Metabolomic analyses revealed 145, 178, and 88 differentially accumulated metabolites (DAMs) in the BBL/ZH58, BFL-1/ZH58, and BFL-2/ZH58×CH72 comparisons, respectively. KEGG pathway enrichment analysis showed that most of the DAMs are involved in biosynthesis of amino acids, and in arginine and proline metabolism. Three co-DEPs and 11 co-DAMs were identified in the seeds of these GM maize lines. The proteomic profiling of seeds showed that the GM maize varieties were not dramatically different from their non-GM control. Similarly, the metabolomic profiling of seeds showed no dramatic changes in the GM/non-GM maize varieties compared with the GM/GM and non-GM/non-GM maize varieties. The genetic background of the transgenic maize was found to have some influence on its proteomic and metabolomic profiles.
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Affiliation(s)
| | | | | | | | | | | | - Wujun Jin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Ectopic Expression of Arabidopsis thaliana zDof1.3 in Tomato ( Solanum lycopersicum L.) Is Associated with Improved Greenhouse Productivity and Enhanced Carbon and Nitrogen Use. Int J Mol Sci 2022; 23:ijms231911229. [PMID: 36232530 PMCID: PMC9570051 DOI: 10.3390/ijms231911229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
A large collection of transgenic tomato lines, each ectopically expressing a different Arabidopsis thaliana transcription factor, was screened for variants with alterations in leaf starch. Such lines may be affected in carbon partitioning, and in allocation to the sinks. We focused on ‘L4080’, which harbored an A. thaliana zDof (DNA-binding one zinc finger) isoform 1.3 (AtzDof1.3) gene, and which had a 2−4-fold higher starch-to-sucrose ratio in source leaves over the diel (p < 0.05). Our aim was to determine whether there were associated effects on productivity. L4080 plants were altered in nitrogen (N) and carbon (C) metabolism. The N-to-C ratio was higher in six-week-old L4080, and when treated with 1/10 N, L4080 growth was less inhibited compared to the wild-type and this was accompanied by faster root elongation (p < 0.05). The six-week-old L4080 acquired 42% more dry matter at 720 ppm CO2, compared to ambient CO2 (p < 0.05), while the wild-type (WT) remained unchanged. GC-MS-TOF data showed that L4080 source leaves were enriched in amino acids compared to the WT, and at 49 DPA, fruit had 25% greater mass, higher sucrose, and increased yield (25%; p < 0.05) compared to the WT. An Affymetrix cDNA array analysis suggested that only 0.39% of the 9000 cDNAs were altered by 1.5-fold (p < 0.01) in L4080 source leaves. 14C-labeling of fruit disks identified potential differences in 14-DPA fruit metabolism suggesting that post-transcriptional regulation was important. We conclude that AtzDof1.3 and the germplasm derived therefrom, should be investigated for their ‘climate-change adaptive’ potential.
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Zhang W, Wang Y, Zhang T, Zhang J, Shen L, Zhang B, Ding C, Su X. Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments. Front Bioeng Biotechnol 2022; 10:929681. [PMID: 35774064 PMCID: PMC9237257 DOI: 10.3389/fbioe.2022.929681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.
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Affiliation(s)
- Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Nanchang Institute of Technology, Nanchang, China
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Le Shen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Changjun Ding, ; Xiaohua Su,
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Integration of the Physiology, Transcriptome and Proteome Reveals the Molecular Mechanism of Drought Tolerance in Cupressus gigantea. FORESTS 2022. [DOI: 10.3390/f13030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Drought stress can dramatically impair woody plant growth and restrict the geographical distribution of many tree species. To better understand the dynamics between the response and mechanism of Cupressus gigantea to drought and post-drought recovery, a comparative analysis was performed, relying on physiological measurements, RNA sequencing (RNA-Seq) and two-dimensional gel electrophoresis (2-DE) proteins. In this study, the analyses revealed that photosynthesis was seriously inhibited, while osmolyte contents, antioxidant enzyme activity and non-enzymatic antioxidant contents were all increased under drought stress in seedlings. Re-watering led to a recovery in most of the parameters analyzed, mainly the photosynthetic parameters and osmolyte contents. Transcriptomic and proteomic profiling suggested that most of the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were specifically altered, and a few were consistently altered. Drought induced a common reduction in the level of DEGs and DEPs associated with photosynthesis. Notably, DEGs and DEPs involved in reactive oxygen species (ROS) scavenging, such as ascorbate oxidase and superoxide dismutase (SOD), showed an inverse pattern under desiccation. This study may improve our understanding of the underlying molecular mechanisms of drought resistance in C. gigantea and paves the way for more detailed molecular analysis of the candidate genes.
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Huang C, Wang Z, Zhu P, Wang C, Wang C, Xu W, Li Z, Fu W, Zhu S. RNA Interference-Based Genetic Engineering Maize Resistant to Apolygus lucorum Does Not Manifest Unpredictable Unintended Effects Relative to Conventional Breeding: Short Interfering RNA, Transcriptome, and Metabolome Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:745708. [PMID: 35283891 PMCID: PMC8908210 DOI: 10.3389/fpls.2022.745708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
Abstract
The use of omics techniques to analyze the differences between genetic engineering organisms and their parents can identify unintended effects and explore whether such unintended effects will have negative consequences. In order to evaluate whether genetic engineering will cause changes in crops beyond the changes introduced by conventional plant breeding, we compared the extent of transcriptome and metabolome modification in the leaves of three lines developed by RNA interference (RNAi)-based genetic engineering and three lines developed by conventional breeding. The results showed that both types of plant breeding methods can manifest changes at the short interfering RNA (siRNA), transcriptomic, and metabolic levels. Relative expression analysis of potential off-target gene revealed that there was no broad gene decline in the three RNAi-based genetic engineering lines. We found that the number of DEGs and DAMs between RNAi-based genetic engineering lines and the parental line was less than that between conventional breeding lines. These unique DEGs and DAMs between RNAi-based genetic engineering lines and the parental lines were not enriched in detrimental metabolic pathways. The results suggest that RNAi-based genetic engineering do not cause unintended effects beyond those found in conventional breeding in maize.
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Affiliation(s)
- Chunmeng Huang
- College of Plant Protection, China Agricultural University, Beijing, China
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhi Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Chenguang Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Chaonan Wang
- College of Plant Protection, China Agricultural University, Beijing, China
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Wenjie Xu
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Wei Fu
- Chinese Academy of Inspection and Quarantine, Beijing, China
- *Correspondence: Wei Fu,
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, China
- Shuifang Zhu,
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11
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Zanon Agapito-Tenfen S, Guerra MP, Nodari RO, Wikmark OG. Untargeted Proteomics-Based Approach to Investigate Unintended Changes in Genetically Modified Maize for Environmental Risk Assessment Purpose. FRONTIERS IN TOXICOLOGY 2021; 3:655968. [PMID: 35295118 PMCID: PMC8915820 DOI: 10.3389/ftox.2021.655968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Abstract
Profiling technologies, such as proteomics, allow the simultaneous measurement and comparison of thousands of plant components without prior knowledge of their identity. The combination of these non-targeted methods facilitates a more comprehensive approach than targeted methods and thus provides additional opportunities to identify genotypic changes resulting from genetic modification, including new allergens or toxins. The purpose of this study was to investigate unintended changes in GM Bt maize grown in South Africa. In the present study, we used bi-dimensional gel electrophoresis based on fluorescence staining, coupled with mass spectrometry in order to compare the proteome of the field-grown transgenic hybrid (MON810) and its near-isogenic counterpart. Proteomic data showed that energy metabolism and redox homeostasis were unequally modulated in GM Bt and non-GM maize variety samples. In addition, a potential allergenic protein—pathogenesis related protein −1 has been identified in our sample set. Our data shows that the GM variety is not substantially equivalent to its non-transgenic near-isogenic variety and further studies should be conducted in order to address the biological relevance and the potential risks of such changes. These finding highlight the suitability of unbiased profiling approaches to complement current GMO risk assessment practices worldwide.
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Affiliation(s)
- Sarah Zanon Agapito-Tenfen
- GenØk Centre for Biosafety, Tromsø, Norway
- *Correspondence: Sarah Zanon Agapito-Tenfen ; orcid.org/0000-0002-9773-0856
| | - Miguel Pedro Guerra
- CropScience Department, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rubens Onofre Nodari
- CropScience Department, Federal University of Santa Catarina, Florianópolis, Brazil
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Almeida MF, Tavares CS, Araújo EO, Picanço MC, Oliveira EE, Pereira EJG. Plant Resistance in Some Modern Soybean Varieties May Favor Population Growth and Modify the Stylet Penetration of Bemisia tabaci (Hemiptera: Aleyrodidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:970-978. [PMID: 33625491 DOI: 10.1093/jee/toab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Indexed: 06/12/2023]
Abstract
Complaints of severe damage by whiteflies in soybean fields containing genetically engineered (GE) varieties led us to investigate the role of transgenic soybean varieties expressing resistance to some insects (Cry1Ac Bt toxin) and to herbicide (glyphosate) on the population growth and feeding behavior of Bemisia tabaci (Gennadius) MEAM1 (Hemiptera: Aleyrodidae). In the laboratory, the whiteflies reared on the GE Bt soybeans had a net reproductive rate (R0) 100% higher and intrinsic rate of population increase (rm) 15% higher than those reared on non-GE soybeans. The increased demographic performance was associated with a higher lifetime fecundity. In electrical penetration graphs, the whiteflies reared on the GE soybeans had fewer probes and spent 50% less time before reaching the phloem phase from the beginning of the first successful probe, indicating a higher risk of transmission of whitefly-borne viruses. Data from Neotropical fields showed a higher population density of B. tabaci on two soybean varieties expressing glyphosate resistance and Cry1Ac Bt toxin. These results indicate that some GE soybean varieties expressing insect and herbicide resistances can be more susceptible to whiteflies than non-GE ones or those only expressing herbicide resistance. Most likely, these differences are related to varietal features that increase host-plant susceptibility to whiteflies. Appropriate pest management may be needed to deal with whiteflies in soybean fields, especially in warm regions, and breeders may want to consider the issue when developing new soybean varieties.
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Affiliation(s)
- Mauricélia F Almeida
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- Center for Agricultural Sciences, Universidade Estadual da Região Tocantina do Maranhão, Imperatriz, MA, Brazil
| | - Clébson S Tavares
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Euires O Araújo
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo C Picanço
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eugênio E Oliveira
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eliseu José G Pereira
- Department of Entomology, Universidade Federal de Viçosa, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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13
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Engineered Maize Hybrids with Diverse Carotenoid Profiles and Potential Applications in Animal Feeding. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33783733 DOI: 10.1007/978-981-15-7360-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Multi-gene transformation methods need to be able to introduce multiple transgenes into plants in order to reconstitute a transgenic locus where the introduced genes express in a coordinated manner and do not segregate in subsequent generations. This simultaneous multiple gene transfer enables the study and modulation of the entire metabolic pathways and the elucidation of complex genetic control circuits and regulatory hierarchies. We used combinatorial nuclear transformation to produce multiplex-transgenic maize plants. In proof of principle experiments, we co-expressed five carotenogenic genes in maize endosperm. The resulting combinatorial transgenic maize plant population, equivalent to a "mutant series," allowed us to identify and complement rate-limiting steps in the extended endosperm carotenoid pathway and to recover corn plants with extraordinary levels of β-carotene and other nutritionally important carotenoids. We then introgressed the induced (transgenic) carotenoid pathway in a transgenic line accumulating high levels of nutritionally important carotenoids into a wild-type yellow-endosperm variety with a high β:ε ratio. Novel hybrids accumulated zeaxanthin at unprecedented amounts. We introgressed the same pathway into a different yellow corn line with a low β:ε ratio. The resulting hybrids, in this case, had a very different carotenoid profile. The role of genetic background in determining carotenoid profiles in corn was elucidated, and further rate-limiting steps in the pathway were identified and resolved in hybrids. Astaxanthin accumulation was engineered by overexpression of a β-carotene ketolase in maize endosperm. In early experiments, limited astaxanthin accumulation in transgenic maize plants was attributed to a bottleneck in the conversion of adonixanthin (4-ketozeaxanthin) to astaxanthin. More recent experiments showed that a synthetic β-carotene ketolase with a superior β-carotene/zeaxanthin ketolase activity is critical for the high-yield production of astaxanthin in maize endosperm. Engineered lines were used in animal feeding experiments which demonstrated not only the safety of the engineered lines but also their efficacy in a range of different animal production applications.
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Perez-Sanz F, Ruiz-Hernández V, Terry MI, Arce-Gallego S, Weiss J, Navarro PJ, Egea-Cortines M. gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites. Metabolites 2021; 11:metabo11040211. [PMID: 33807334 PMCID: PMC8065537 DOI: 10.3390/metabo11040211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using standard Excel output files from an Agilent Chemstation GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR has two filters for data preprocessing removing contaminants and low-quality peaks. The first function NormalizeWithinFiles, samples assigning retention times to CAS. The second function NormalizeBetweenFiles, reaches a consensus between files where compounds in close retention times are grouped together. The third function getGroups, establishes what is considered as Constitutive Profile, Non-constitutive by Frequency i.e., not present in all samples and Non-constitutive by Quality. Results can be plotted with the plotGroup function. We used it to analyse floral scent emissions in four snapdragon genotypes. These included a wild type, Deficiens nicotianoides and compacta affecting floral identity and RNAi:AmLHY targeting a circadian clock gene. We identified differences in scent constitutive and non-constitutive profiles as well as in timing of emission. gcProfileMakeR is a very useful tool to define constitutive and non-constitutive scent profiles. It also allows to analyse genotypes and circadian datasets to identify differing metabolites.
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Affiliation(s)
- Fernando Perez-Sanz
- Instituto Murciano de Investigaciones Biomédicas El Palmar, 30120 Murcia, Spain;
| | | | - Marta I. Terry
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (M.I.T.); (J.W.)
| | | | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (M.I.T.); (J.W.)
| | - Pedro J. Navarro
- DSIE Cuartel de Antiguones, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain;
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (M.I.T.); (J.W.)
- Correspondence: ; Tel.: +34-868071078
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15
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Metabolic Analysis Reveals Cry1C Gene Transformation Does Not Affect the Sensitivity of Rice to Rice Dwarf Virus. Metabolites 2021; 11:metabo11040209. [PMID: 33808359 PMCID: PMC8065979 DOI: 10.3390/metabo11040209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Metabolomics is beginning to be used for assessing unintended changes in genetically modified (GM) crops. To investigate whether Cry1C gene transformation would induce metabolic changes in rice plants, and whether the metabolic changes would pose potential risks when Cry1C rice plants are exposed to rice dwarf virus (RDV), the metabolic profiles of Cry1C rice T1C-19 and its non-Bt parental rice MH63 under RDV-free and RDV-infected status were analyzed using gas chromatography–mass spectrometry (GC-MS). Compared to MH63 rice, slice difference was detected in T1C-19 under RDV-free conditions (less than 3%), while much more metabolites showed significant response to RDV infection in T1C-19 (15.6%) and in MH63 (5.0%). Pathway analysis showed biosynthesis of lysine, valine, leucine, and isoleucine may be affected by RDV infection in T1C-19. No significant difference in the contents of free amino acids (AAs) was found between T1C-19 and MH63 rice, and the free AA contents of the two rice plants showed similar responses to RDV infection. Furthermore, no significant differences of the RDV infection rates between T1C-19 and MH63 were detected. Our results showed the Cry1C gene transformation did not affect the sensitivity of rice to RDV, indicating Cry1C rice would not aggravate the epidemic and dispersal of RDV.
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16
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Liu W, Chen H, Li L, Dong M, Zhang Z, Wan Y, Jin W. Proteomic analysis of the seeds of transgenic rice lines and the corresponding nongenetically modified isogenic variety. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1869-1878. [PMID: 32898281 DOI: 10.1002/jsfa.10802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND An isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis was employed to study the seeds of two genetically modified (GM) rice lines, T2A-1 and T1C-19, and their nontransgenic isogenic variety, MH63, to investigate the unintended effects of genetic modification. RESULTS A total of 3398 proteins were quantitatively identified. Seventy-seven differentially abundant proteins (DAPs) were identified in the T2A-1/MH63 comparison, and 70 and 7 of these DAPs were upregulated and downregulated, respectively. A pathway enrichment analysis showed that most of these DAPs participated in metabolic pathways and protein processing in endoplasmic reticulum and were ribosome components. Some 181 DAPs were identified from the T1C-19/MH63 comparison, and these included 115 upregulated proteins and 66 downregulated proteins. The subsequent pathway enrichment analysis showed that these DAPs mainly participated in protein processing in endoplasmic reticulum and carbon fixation in photosynthetic organisms and were ribosome components. None of these DAPs were identified as new unintended toxins or allergens, and only changes in abundance were detected. Fifty-four co-DAPs were identified in the seeds of the two GM rice lines, and protein-protein interaction analysis of these co-DAPs demonstrated that some interacting proteins were involved in protein processing in endoplasmic reticulum and metabolic pathways, whereas others were identified as ribosome components. Representative co-DAPs and proteins related to nutrients were analyzed using qRT-PCR to determine their transcriptional levels. CONCLUSIONS The results suggested that the seed proteomic profiles of the two GM rice lines studied were not substantially altered from those of their natural isogenic control. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Hao Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Mei Dong
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Zhe Zhang
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Yusong Wan
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, PR China
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17
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Liu W, Zhao H, Miao C, Jin W. Integrated proteomics and metabolomics analysis of transgenic and gene-stacked maize line seeds. GM CROPS & FOOD 2021; 12:361-375. [PMID: 34097556 PMCID: PMC8189116 DOI: 10.1080/21645698.2021.1934351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Unintended effects of genetically modified (GM) crops may pose safety issues. Omics techniques provide researchers with useful tools to assess such unintended effects. Proteomics and metabolomics analyses were performed for three GM maize varieties, 2A-7, CC-2, and 2A-7×CC-2 stacked transgenic maize, and the corresponding non-GM parent Zheng58.Proteomics revealed 120, 271 and 135 maize differentially expressed proteins (DEPs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEPs participated in metabolic pathways and the biosynthesis of secondary metabolite. Metabolomics revealed 179, 135 and 131 differentially accumulated metabolites (DAMs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Based on KEGG enrichment analysis, most DAMs are involved in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated proteomics and metabolomics analysis, the introduction of exogenous EPSPS did not affect the expression levels of six other enzymes or the abundance of seven metabolites involved in the shikimic acid pathway in CC-2 and 2A-7×CC-2 seeds. Six co-DEPs annotated by integrated proteomics and metabolomics pathway analysis were further analyzed by qRT-PCR.This study successfully employed integrated proteomic and metabolomic technology to assess unintended changes in maize varieties. The results suggest that GM and gene stacking do not cause significantly unintended effects.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Chaohua Miao
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, P.R. China
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18
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Zhang X, Zhang R, Li L, Yang Y, Ding Y, Guan H, Wang X, Zhang A, Wen H. Negligible transcriptome and metabolome alterations in RNAi insecticidal maize against Monolepta hieroglyphica. PLANT CELL REPORTS 2020; 39:1539-1547. [PMID: 32869121 PMCID: PMC7554010 DOI: 10.1007/s00299-020-02582-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/17/2020] [Indexed: 06/01/2023]
Abstract
RNAi-based genetically modified maize resistant to Monolepta hieroglyphica (Motschulsky) was demonstrated with negligible transcriptome and metabolome alterations compared to its unmodified equivalent. As one of the most prevalent insect pests afflicting various crops, Monolepta hieroglyphica (Motschulsky) causes severe loss of agricultural and economic productivity for many years in China. In an effort to reduce damages, in this study, an RNA interference (RNAi)-based genetically modified (GM) maize was developed. It was engineered to produce MhSnf7 double-stranded RNAs (dsRNAs), which can suppress the Snf7 gene expression and then lead M. hieroglyphica to death. Field trail analysis confirmed the robustly insecticidal ability of the MhSnf7 GM maize to resist damages by M. hieroglyphica. RNA sequencing analysis identified that only one gene was differentially expressed in the MhSnf7 GM maize compared to non-GM maize, indicating that the transcriptome in MhSnf7 GM maize is principally unaffected by the introduction of the MhSnf7 dsRNA expression vector. Likewise, metabolomics analysis identified that only 8 out of 5787 metabolites were significantly changed. Hence, the integration of transcriptomics and metabolomics demonstrates that there are negligible differences between MhSnf7 GM maize and its unmodified equivalent. This study not only presents a comprehensive assessment of cellular alteration in terms of gene transcription and metabolite abundance in RNAi-based GM maize, but also could be used as a reference for evaluating the unintended effect of GM crops.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Yang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yijia Ding
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Haitao Guan
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaoqin Wang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Aihong Zhang
- Beijing DaBeiNong Biotechnology Co., Ltd., Beijing, 100080, China
| | - Hongtao Wen
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
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Bedair M, Glenn KC. Evaluation of the use of untargeted metabolomics in the safety assessment of genetically modified crops. Metabolomics 2020; 16:111. [PMID: 33037482 PMCID: PMC7547035 DOI: 10.1007/s11306-020-01733-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/29/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND The safety assessment of foods and feeds from genetically modified (GM) crops includes the comparison of key characteristics, such as crop composition, agronomic phenotype and observations from animal feeding studies compared to conventional counterpart varieties that have a history of safe consumption, often including a near isogenic variety. The comparative compositional analysis of GM crops has been based on targeted, validated, quantitative analytical methods for the key food and feed nutrients and antinutrients for each crop, as identified by Organization of Economic Co-operation and Development (OCED). As technologies for untargeted metabolomic methods have evolved, proposals have emerged for their use to complement or replace targeted compositional analytical methods in regulatory risk assessments of GM crops to increase the number of analyzed metabolites. AIM OF REVIEW The technical opportunities, challenges and strategies of including untargeted metabolomics analysis in the comparative safety assessment of GM crops are reviewed. The results from metabolomics studies of GM and conventional crops published over the last eight years provide context to enable the discussion of whether metabolomics can materially improve the risk assessment of food and feed from GM crops beyond that possible by the Codex-defined practices used worldwide for more than 25 years. KEY SCIENTIFIC CONCEPTS OF REVIEW Published studies to date show that environmental and genetic factors affect plant metabolomics profiles. In contrast, the plant biotechnology process used to make GM crops has little, if any consequence, unless the inserted GM trait is intended to alter food or feed composition. The nutritional value and safety of food and feed from GM crops is well informed by the quantitative, validated compositional methods for list of key analytes defined by crop-specific OECD consensus documents. Untargeted metabolic profiling has yet to provide data that better informs the safety assessment of GM crops than the already rigorous Codex-defined quantitative comparative assessment. Furthermore, technical challenges limit the implementation of untargeted metabolomics for regulatory purposes: no single extraction method or analytical technique captures the complete plant metabolome; a large percentage of metabolites features are unknown, requiring additional research to understand if differences for such unknowns affect food/feed safety; and standardized methods are needed to provide reproducible data over time and laboratories.
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20
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Brown AJ, Newhouse AE, Powell WA, Parry D. Comparative efficacy of gypsy moth (Lepidoptera: Erebidae) entomopathogens on transgenic blight-tolerant and wild-type American, Chinese, and hybrid chestnuts (Fagales: Fagaceae). INSECT SCIENCE 2020; 27:1067-1078. [PMID: 31339228 DOI: 10.1111/1744-7917.12713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
American chestnut (Castanea dentata [Marsh.] Borkh.) was once the dominant hardwood species in Eastern North America before an exotic fungal pathogen, Cryphonectria parasitica (Murrill) Barr, functionally eliminated it across its range. One promising approach toward restoring American chestnut to natural forests is development of blight-tolerant trees using genetic transformation. However, transformation and related processes can result in unexpected and unintended phenotypic changes, potentially altering ecological interactions. To assess unintended tritrophic impacts of transgenic American chestnut on plant-herbivore interactions, gypsy moth (Lymantria dispar L.) caterpillars were fed leaf disks excised from two transgenic events, Darling 54 and Darling 58, and four control American chestnut lines. Leaf disks were previously treated with an LD50 dose of either the species-specific Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) or the generalist pathogen Bacillus thuringiensis subsp. kurstaki (Btk). Mortality was quantified and compared to water blank controls. Tree genotype had a strong effect on the efficacies of both pathogens. Larval mortality from Btk-treated foliage from only one transgenic event, Darling 54, differed from its isogenic progenitor, Ellis 1, but was similar to an unrelated wild-type American chestnut control. LdMNPV efficacy was unaffected by genetic transformation. Results suggest that although genetic modification of trees may affect interactions with other nontarget organisms, this may be due to insertion effects, and variation among different genotypes (whether transgenic or wild-type) imparts a greater change in response than transgene presence.
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Affiliation(s)
- Aaron J Brown
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Andrew E Newhouse
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - William A Powell
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Dylan Parry
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
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21
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iTRAQ-based quantitative proteomic analysis of transgenic and non-transgenic maize seeds. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Liu Q, Yang X, Tzin V, Peng Y, Romeis J, Li Y. Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2236-2249. [PMID: 32593184 PMCID: PMC7540705 DOI: 10.1111/tpj.14895] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 05/09/2023]
Abstract
Advancements in -omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and high-performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross-breeding in rice.
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Affiliation(s)
- Qingsong Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
- College of Life SciencesXinyang Normal UniversityXinyang464000People’s Republic of China
| | - Xiaowei Yang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of DrylandsJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSede Boqer CampusMidreseht Ben Gurion8499000Israel
| | - Yufa Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
| | - Jörg Romeis
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
- Agroscope, Research Division Agroecology and EnvironmentZurich8046Switzerland
| | - Yunhe Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
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Fedorova M, Herman RA. Obligatory metabolomic profiling of gene-edited crops is risk disproportionate. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1985-1988. [PMID: 32593232 PMCID: PMC7540486 DOI: 10.1111/tpj.14896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/06/2023]
Abstract
It has been argued that the application of metabolomics to gene-edited crops would present value in three areas: (i) the detection of gene-edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk-disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene-edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.
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Affiliation(s)
- Maria Fedorova
- Corteva Agriscience7100 NW 62 AvePO Box 1000JohnstonIA50131USA
| | - Rod A. Herman
- Corteva Agriscience9330 Zionsville RoadIndianapolisIN46268USA
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Muzhinji N, Ntuli V. Genetically modified organisms and food security in Southern Africa: conundrum and discourse. GM CROPS & FOOD 2020; 12:25-35. [PMID: 32687427 PMCID: PMC7553747 DOI: 10.1080/21645698.2020.1794489] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The importance of food security and nourishment is recognized in Southern African region and in many communities, globally. However, the attainment of food security in Southern African countries is affected by many factors, including adverse environmental conditions, pests and diseases. Scientists have been insistently looking for innovative strategies to optimize crop production and combat challenges militating against attainment of food security. In agriculture, strategies of increasing crop production include but not limited to improved crop varieties, farming practices, extension services, irrigation services, mechanization, information technology, use of fertilizers and agrochemicals. Equally important is genetic modification (GM) technology, which brings new prospects in addressing food security problems. Nonetheless, since the introduction of genetically modified crops (GMOs) three decades ago, it has been a topic of public discourse across the globe, conspicuously so in Southern African region. This is regardless of the evidence that planting GMOs positively influenced farmer’s incomes, economic access to food and increased tolerance of crops to various biotic and abiotic stresses. This paper looks at the issues surrounding GMOs adoption in Southern Africa and lack thereof, the discourse, and its potential in contributing to the attainment of food security for the present as well as future generations.
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Affiliation(s)
- Norman Muzhinji
- Department of Natural and Applied Sciences, Namibia University of Science and Technology , Windhoek, Namibia
| | - Victor Ntuli
- Department of Biology, National University of Lesotho , Roma, Lesotho
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25
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Raybould A. Problem formulation and phenotypic characterisation for the development of novel crops. Transgenic Res 2020; 28:135-145. [PMID: 31321696 DOI: 10.1007/s11248-019-00147-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypic characterisation provides important information about novel crops that helps their developers to make technical and commercial decisions. Phenotypic characterisation comprises two activities. Product characterisation checks that the novel crop has the qualities of a viable product-the intended traits have been introduced and work as expected, and no unintended changes have been made that will adversely affect the performance of the final product. Risk assessment evaluates whether the intended and unintended changes are likely to harm human health or the environment. Product characterisation follows the principles of problem formulation, namely that the characteristics required in the final product are defined and criteria to decide whether the novel crop will have these properties are set. The hypothesis that the novel crop meets the criteria are tested during product development. If the hypothesis is corroborated, development continues, and if the hypothesis is falsified, the product is redesigned or its development is halted. Risk assessment should follow the same principles. Criteria that indicate the crop poses unacceptable risk should be set, and the hypothesis that the crop does not possess those properties should be tested. However, risk assessment, particularly when considering unintended changes introduced by new plant breeding methods such as gene editing, often ignores these principles. Instead, phenotypic characterisation seeks to catalogue all unintended changes by profiling methods and then proceeds to work out whether any of the changes are important. This paper argues that profiling is an inefficient and ineffective method of phenotypic characterisation for risk assessment. It discusses reasons why profiling is favoured and corrects some misconceptions about problem formulation.
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Affiliation(s)
- Alan Raybould
- Syngenta Crop Protection AG, Rosentalstrasse 67, 4002, Basel, Switzerland.
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Liu W, Zhang Z, Liu X, Jin W. iTRAQ-based quantitative proteomic analysis of two transgenic soybean lines and the corresponding non-genetically modified isogenic variety. J Biochem 2020; 167:67-78. [PMID: 31596463 DOI: 10.1093/jb/mvz081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/27/2019] [Indexed: 11/14/2022] Open
Abstract
To investigate the unintended effects of genetically modified (GM) crops, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed with seed cotyledons of two GM soybean lines, MON87705 and MON87701×MON89788, and the corresponding non-transgenic isogenic variety A3525. Thirty-five differentially abundant proteins (DAPs) were identified in MON87705/A3525, 27 of which were upregulated and 8 downregulated. Thirty-eight DAPs were identified from the MON87701×MON89788/A3525 sample, including 29 upregulated proteins and 9 downregulated proteins. Pathway analysis showed that most of these DAPs participate in protein processing in endoplasmic reticulum and in metabolic pathways. Protein-protein interaction analysis of these DAPs demonstrated that the main interacting proteins are associated with post-translational modification, protein turnover, chaperones and signal transduction mechanisms. Nevertheless, these DAPs were not identified as new unintended toxins or allergens and only showed changes in abundance. All these results suggest that the seed cotyledon proteomic profiles of the two GM soybean lines studied were not dramatically altered compared with that of their natural isogenic control.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
| | - Zhe Zhang
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
| | - Xuri Liu
- Department of Food and Biological Engineering, Handan Polytechnic College, No.141 Zhuhe Road, Hanshan District, Handan, P.R. China
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, No. 12 Zhongguancun South St., Haidian District, Beijing, P.R. China
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Corujo M, Pla M, van Dijk J, Voorhuijzen M, Staats M, Slot M, Lommen A, Barros E, Nadal A, Puigdomènech P, Paz JLL, van der Voet H, Kok E. Use of omics analytical methods in the study of genetically modified maize varieties tested in 90 days feeding trials. Food Chem 2019; 292:359-371. [DOI: 10.1016/j.foodchem.2018.05.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/04/2018] [Accepted: 05/24/2018] [Indexed: 10/16/2022]
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Raybould A, Holt K, Kimber I. Using problem formulation to clarify the meaning of weight of evidence and biological relevance in environmental risk assessments for genetically modified crops. GM CROPS & FOOD 2019; 10:63-76. [PMID: 31184249 PMCID: PMC6615591 DOI: 10.1080/21645698.2019.1621615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/13/2022]
Abstract
Weight of evidence and biological relevance are important concepts for risk assessment and decision-making over the use of GM crops; however, their meanings are not well defined. We use problem formulation to clarify the definition of these concepts and thereby identify data that are relevant for risk assessment. Problem formulation defines criteria for the acceptability of risk and devises rigorous tests of the hypothesis that the criteria are met. Corroboration or falsification of such hypotheses characterize risk and enable predictable and transparent decisions about whether certain risks from using a particular GM crop are acceptable. Decisions based on a weight of evidence approach use a synthesis of several lines of evidence, whereas a "definitive" approach to risk assessment enables some decisions to be based on the results of a single test. Data are biologically relevant for risk assessment only if they test a hypothesis that is useful for decision-making.
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Affiliation(s)
| | - Karen Holt
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, UK
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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Kang W, Li X, Sun A, Yu F, Hu X. Study of the Persistence of the Phytotoxicity Induced by Graphene Oxide Quantum Dots and of the Specific Molecular Mechanisms by Integrating Omics and Regular Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3791-3801. [PMID: 30870590 DOI: 10.1021/acs.est.8b06023] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although increasing attention has been paid to the nanotoxicity of graphene oxide quantum dots (GOQDs) due to their broad range of applications, the persistence and recoverability associated with GOQDs had been widely ignored. Interestingly, stress-response hormesis for algal growth was observed for Chlorella vulgaris as a single-celled model organism. Few physiological parameters, such as algal density, plasmolysis, and levels of reactive oxygen species, exhibited facile recovery. In contrast, the effects on chlorophyll a levels, permeability, and starch grain accumulation exhibited persistent toxicity. In the exposure stage, the downregulation of genes related to unsaturated fatty acid biosynthesis, carotenoid biosynthesis, phenylpropanoid biosynthesis, and binding contributed to toxic effects on photosynthesis. In the recovery stage, downregulation of genes related to the cis-Golgi network, photosystem I, photosynthetic membrane, and thylakoid was linked to the persistence of toxic effects on photosynthesis. The upregulated galactose metabolism and downregulated aminoacyl-tRNA biosynthesis also indicated toxicity persistence in the recovery stage. The downregulation and upregulation of phenylalanine metabolism in the exposure and recovery stages, respectively, reflected the tolerance of the algae to GOQDs. The present study highlights the importance of studying nanotoxicity by elucidation of stress and recovery patterns with metabolomics and transcriptomics.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering , Nankai University , Tianjin 300350 , P. R. China
| | - Xiaokang Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering , Nankai University , Tianjin 300350 , P. R. China
| | - Anqi Sun
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering , Nankai University , Tianjin 300350 , P. R. China
| | - Fubo Yu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering , Nankai University , Tianjin 300350 , P. R. China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering , Nankai University , Tianjin 300350 , P. R. China
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KhalKhal E, Rezaei-Tavirani M, Rostamii-Nejad M. Pharmaceutical Advances and Proteomics Researches. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:51-67. [PMID: 32802089 PMCID: PMC7393046 DOI: 10.22037/ijpr.2020.112440.13758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proteomics enables understanding the composition, structure, function and interactions of the entire protein complement of a cell, a tissue, or an organism under exactly defined conditions. Some factors such as stress or drug effects will change the protein pattern and cause the present or absence of a protein or gradual variation in abundances. The aim of this study is to explore relationship between proteomics application and drug discovery. "proteomics", "Application", and "pharmacology were the main keywords that were searched in PubMed (PubMed Central), Web of Science, and Google Scholar. The titles that were stablished by 2019, were studied and after study of the appreciated abstracts, the full texts of the 118 favor documents were extracted. Changes in the proteome provide a snapshot of the cell activities and physiological processes. Proteomics shows the observed protein changes to the causal effects and generate a complete three-dimensional map of the cell indicating their exact location. Proteomics is used in different biological fields and is applied in medicine, agriculture, food microbiology, industry, and pharmacy and drug discovery. Biomarker discovery, follow up of drug effect on the patients, and in vitro and in vivo proteomic investigation about the drug treated subjects implies close relationship between proteomics advances and application and drug discovery and development. This review overviews and summarizes the applications of proteomics especially in pharmacology and drug discovery.
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Affiliation(s)
- Ensieh KhalKhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Rostamii-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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31
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Zhou D, Liu X, Gao S, Guo J, Su Y, Ling H, Wang C, Li Z, Xu L, Que Y. Foreign cry1Ac gene integration and endogenous borer stress-related genes synergistically improve insect resistance in sugarcane. BMC PLANT BIOLOGY 2018; 18:342. [PMID: 30526526 PMCID: PMC6288918 DOI: 10.1186/s12870-018-1536-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Sugarcane (Saccharum spp. hybrids) is considered the most globally important sugar-producing crop and raw material for biofuel. Insect attack is a major issue in sugarcane cultivation, resulting in yield losses and sucrose content reductions. Stem borer (Diatraea saccharalis F.) causes serious yield losses in sugarcane worldwide. However, insect-resistant germplasms for sugarcane are not available in any collections all over the world, and the molecular mechanism of insect resistance has not been elucidated. In this study, cry1Ac transgenic sugarcane lines were obtained and the biological characteristics and transgene dosage effect were investigated and a global exploration of gene expression by transcriptome analysis was performed. RESULTS The transgene copies of foreign cry1Ac were variable and random. The correlation between the cry1Ac protein and cry1Ac gene copies differed between the transgenic lines from FN15 and ROC22. The medium copy lines from FN15 showed a significant linear relationship, while ROC22 showed no definite dosage effect. The transgenic lines with medium copies of cry1Ac showed an elite phenotype. Transcriptome analysis by RNA sequencing indicated that up/down regulated differentially expressed genes were abundant among the cry1Ac sugarcane lines and the receptor variety. Foreign cry1Ac gene and endogenous borer stress-related genes may have a synergistic effect. Three lines, namely, A1, A5, and A6, were selected for their excellent stem borer resistance and phenotypic traits and are expected to be used directly as cultivars or crossing parents for sugarcane borer resistance breeding. CONCLUSIONS Cry1Ac gene integration dramatically improved sugarcane insect resistance. The elite transgenic offspring contained medium transgene copies. Foreign cry1Ac gene integration and endogenous borer stress-related genes may have a synergistic effect on sugarcane insect resistance improvement.
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Affiliation(s)
- Dinggang Zhou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, Hunan University of Science and Technology, School of Life Science, Xiangtan, 411201 Hunan China
| | - Xiaolan Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, Hunan University of Science and Technology, School of Life Science, Xiangtan, 411201 Hunan China
| | - Shiwu Gao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Hui Ling
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Chunfeng Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Zhu Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002 Fujian China
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Liu W, Xu W, Li L, Dong M, Wan Y, He X, Huang K, Jin W. iTRAQ-based quantitative tissue proteomic analysis of differentially expressed proteins (DEPs) in non-transgenic and transgenic soybean seeds. Sci Rep 2018; 8:17681. [PMID: 30518773 PMCID: PMC6281665 DOI: 10.1038/s41598-018-35996-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/12/2018] [Indexed: 12/29/2022] Open
Abstract
The unintended effects of transgenesis have increased food safety concerns, meriting comprehensive evaluation. Proteomic profiling provides an approach to directly assess the unintended effects. Herein, the isobaric tags for relative and absolute quantitation (iTRAQ) comparative proteomic approach was employed to evaluate proteomic profile differences in seed cotyledons from 4 genetically modified (GM) and 3 natural genotypic soybean lines. Compared with their non-GM parents, there were 67, 61, 13 and 22 differentially expressed proteins (DEPs) in MON87705, MON87701 × MON89788, MON87708, and FG72. Overall, 170 DEPs were identified in the 3 GM soybean lines with the same parents, but 232 DEPs were identified in the 3 natural soybean lines. Thus, the differences in protein expression among the genotypic varieties were greater than those caused by GM. When considering ≥2 replicates, 4 common DEPs (cDEPs) were identified in the 3 different GM soybean lines with the same parents and 6 cDEPs were identified in the 3 natural varieties. However, when considering 3 replicates, no cDEPs were identified. Regardless of whether ≥2 or 3 replicates were considered, no cDEPs were identified among the 4 GM soybean lines. Therefore, no feedback due to GM was observed at the common protein level in this study.
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Affiliation(s)
- Weixiao Liu
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Wentao Xu
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Liang Li
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Mei Dong
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Yusong Wan
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China
| | - Xiaoyun He
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Kunlun Huang
- Laboratory of Food Safety and Molecular Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China.
| | - Wujun Jin
- Biotechnology Research Institute, Chinese Agricultural and Academic Sciences, Beijing, 100081, PR China.
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Ladics GS. Assessment of the potential allergenicity of genetically-engineered food crops. J Immunotoxicol 2018; 16:43-53. [PMID: 30409058 DOI: 10.1080/1547691x.2018.1533904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An extensive safety assessment process exists for genetically-engineered (GE) crops. The assessment includes an evaluation of the introduced protein as well as the crop containing the protein with the goal of demonstrating the GE crop is "as-safe-as" non-GE crops in the food supply. One of the evaluations for GE crops is to assess the expressed protein for allergenic potential. Currently, no single factor is recognized as a predictor for protein allergenicity. Therefore, a weight-of-the-evidence approach, which accounts for a variety of factors and approaches for an overall assessment of allergenic potential, is conducted. This assessment includes an evaluation of the history of exposure and safety of the gene(s) source; protein structure (e.g. amino acid sequence identity to human allergens); stability of the protein to pepsin digestion in vitro; heat stability of the protein; glycosylation status; and when appropriate, specific IgE binding studies with sera from relevant clinically allergic subjects. Since GE crops were first commercialized over 20 years ago, there is no proof that the introduced novel protein(s) in any commercialized GE food crop has caused food allergy.
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Mishra AK, Duraisamy GS, Khare M, Kocábek T, Jakse J, Bříza J, Patzak J, Sano T, Matoušek J. Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors. BMC Genomics 2018; 19:739. [PMID: 30305019 PMCID: PMC6180420 DOI: 10.1186/s12864-018-5125-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 09/27/2018] [Indexed: 01/04/2023] Open
Abstract
Background The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry and are having potential biomedical applications. Several independent breeding programs around the world have been initiated to develop new cultivars with enriched lupulin and secondary metabolite contents but met with limited success due to several constraints. In the present work, a pioneering attempt has been made to overexpress master regulator binary transcription factor complex formed by HlWRKY1 and HlWDR1 using a plant expression vector to enhance the level of prenylflavonoid and bitter acid content in the hop. Subsequently, we performed transcriptional profiling using high-throughput RNA-Seq technology in leaves of resultant transformants and wild-type hop to gain in-depth information about the genome-wide functional changes induced by HlWRKY1 and HlWDR1 overexpression. Results The transgenic WW-lines exhibited an elevated expression of structural and regulatory genes involved in prenylflavonoid and bitter acid biosynthesis pathways. In addition, the comparative transcriptome analysis revealed a total of 522 transcripts involved in 30 pathways, including lipids and amino acids biosynthesis, primary carbon metabolism, phytohormone signaling and stress responses were differentially expressed in WW-transformants. It was apparent from the whole transcriptome sequencing that modulation of primary carbon metabolism and other pathways by HlWRKY1 and HlWDR1 overexpression resulted in enhanced substrate flux towards secondary metabolites pathway. The detailed analyses suggested that none of the pathways or genes, which have a detrimental effect on physiology, growth and development processes, were induced on a genome-wide scale in WW-transgenic lines. Conclusions Taken together, our results suggest that HlWRKY1 and HlWDR1 simultaneous overexpression positively regulates the prenylflavonoid and bitter acid biosynthesis pathways in the hop and thus these transgenes are presented as prospective candidates for achieving enhanced secondary metabolite content in the hop. Electronic supplementary material The online version of this article (10.1186/s12864-018-5125-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Ganesh Selvaraj Duraisamy
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Mudra Khare
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Jindřich Bříza
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Josef Patzak
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 43846, Žatec, Czech Republic
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Department of Applied Biosciences, Hirosaki University, Hirosaki, Aomori, 036-8561, Japan
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic.
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Comments on two recent publications on GM maize and Roundup. Sci Rep 2018; 8:13338. [PMID: 30177715 PMCID: PMC6120907 DOI: 10.1038/s41598-018-30440-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/08/2018] [Indexed: 11/24/2022] Open
Abstract
Two -omics studies on genetically modified maize and Roundup-fed rats, recently published in the journal Scientific Reports, contain serious flaws in the experimental design, methodology and interpretation of results, which we point out here. The use of -omics technologies are of increasing importance in research, however we argue for a cautious approach to the potential application in food safety assessments as these exceptionally sensitive and complex methods require a thorough and detailed evaluation of the biological significance of obtained results. Arising from: Mesnage et al. Sci Rep 7:39328 (2017), Mesnage et al. Sci Rep 6:37855 (2016).
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Pan L, Meng C, Wang J, Ma X, Fan X, Yang Z, Zhou M, Zhang X. Integrated omics data of two annual ryegrass (Lolium multiflorum L.) genotypes reveals core metabolic processes under drought stress. BMC PLANT BIOLOGY 2018; 18:26. [PMID: 29378511 PMCID: PMC5789592 DOI: 10.1186/s12870-018-1239-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Annual ryegrass (Lolium multiflorum L.) is a commercially important, widely distributed forage crop that is used in the production of hay and silage worldwide. Drought has been a severe environmental constraint in its production. Nevertheless, only a handful of studies have examined the impact of short-term drought stress on annual ryegrass. The aim of this study was to explore how stress-induced core metabolic processes enhance drought tolerance, or adaptation to drought, in annual ryegrass. RESULTS We profiled the transcriptomes, proteomes, and metabolomes of two annual ryegrass genotypes: the drought-resistant genotype "Abundant 10" and drought-susceptible genotype "Adrenalin 11." We identified differentially expressed metabolites and their corresponding proteins and transcripts that are involved in 23 core metabolic processes, in response to short-term drought stress. Protein-gene-metabolite correlation networks were built to reveal the relationships between the expression of transcripts, proteins, and metabolites in drought-resistant annual ryegrass. Furthermore, integrated metabolic pathways were used to observe changes in enzymes corresponding with levels of amino acids, lipids, carbohydrate conjugates, nucleosides, alkaloids and their derivatives, and pyridines and their derivatives. The resulting omics data underscored the significance of 23 core metabolic processes on the enhancement of drought tolerance or adaptation to drought in annual ryegrass. CONCLUSIONS The regulatory networks were inferred using MCoA and correlation analysis to reveal the relationships among the expression of transcripts, proteins, and metabolites that highlight the corresponding elements of these core metabolic pathways. Our results provide valuable insight into the molecular mechanisms of drought resistance, and represent a promising strategy toward the improvement of drought tolerance in annual ryegrass.
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Affiliation(s)
- Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Meng
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, USA
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaomei Fan
- Vazyme Biotech Co., Ltd, Nanjing State Economy & Technology Development Zone, Red Maple Technology Industrial Park, Nanjing, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Comparative analysis of miRNA expression profiles in transgenic and non-transgenic rice using miRNA-Seq. Sci Rep 2018; 8:338. [PMID: 29321648 PMCID: PMC5762784 DOI: 10.1038/s41598-017-18723-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/15/2017] [Indexed: 12/02/2022] Open
Abstract
Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches. Although these GM lines have different types of integration sites, copy numbers, and levels of gene expression, 21 differentially expressed miRNAs have been found compared to wild type. There is no correlation between transgenic protein expression level and the quantity of differentially expressed miRNAs. This study provides useful data about the miRNA composition of GM plants, and it might be helpful for future risk assessments of miRNA-based GM plants.
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Nadal A, De Giacomo M, Einspanier R, Kleter G, Kok E, McFarland S, Onori R, Paris A, Toldrà M, van Dijk J, Wal JM, Pla M. Exposure of livestock to GM feeds: Detectability and measurement. Food Chem Toxicol 2017; 117:13-35. [PMID: 28847764 DOI: 10.1016/j.fct.2017.08.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022]
Abstract
This review explores the possibilities to determine livestock consumption of genetically modified (GM) feeds/ingredients including detection of genetically modified organism (GMO)-related DNA or proteins in animal samples, and the documentary system that is in place for GM feeds under EU legislation. The presence and level of GMO-related DNA and proteins can generally be readily measured in feeds, using established analytical methods such as polymerase chain reaction and immuno-assays, respectively. Various technical challenges remain, such as the simultaneous detection of multiple GMOs and the identification of unauthorized GMOs for which incomplete data on the inserted DNA may exist. Given that transfer of specific GMO-related DNA or protein from consumed feed to the animal had seldom been observed, this cannot serve as an indicator of the individual animal's prior exposure to GM feeds. To explore whether common practices, information exchange and the specific GM feed traceability system in the EU would allow to record GM feed consumption, the dairy chain in Catalonia, where GM maize is widely grown, was taken as an example. It was thus found that this system would neither enable determination of an animal's consumption of specific GM crops, nor would it allow for quantitation of the exposure.
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Affiliation(s)
- Anna Nadal
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain.
| | - Marzia De Giacomo
- Department of Veterinary Public Health and Food Safety, GMO and Mycotoxins Unit, Italian National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Gijs Kleter
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Sarah McFarland
- Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Roberta Onori
- Department of Veterinary Public Health and Food Safety, GMO and Mycotoxins Unit, Italian National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alain Paris
- Sorbonne Universités, Muséum National d'Histoire Naturelle, CNRS, UMR7245 MCAM, Paris, France
| | - Mònica Toldrà
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain
| | - Jeroen van Dijk
- RIKILT Wageningen University & Research, Akkermaalsbos 2, 6708WB Wageningen, The Netherlands
| | - Jean-Michel Wal
- AgroParisTech, Institut National de la Recherche Agronomique (INRA), Paris, France
| | - Maria Pla
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003 Girona, Spain
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Khakimov B, Rasmussen MA, Kannangara RM, Jespersen BM, Munck L, Engelsen SB. From metabolome to phenotype: GC-MS metabolomics of developing mutant barley seeds reveals effects of growth, temperature and genotype. Sci Rep 2017; 7:8195. [PMID: 28811511 PMCID: PMC5557882 DOI: 10.1038/s41598-017-08129-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 07/05/2017] [Indexed: 01/16/2023] Open
Abstract
The development of crop varieties tolerant to growth temperature fluctuations and improved nutritional value is crucial due to climate change and global population growth. This study investigated the metabolite patterns of developing barley seed as a function of genotype and growth temperature for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene, causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid cycle, shikimate-phenylpropanoid pathway, mevalonate, lipid and carbohydrate metabolism were observed for the barley mutants, whereas growth temperature primarily affected shikimate-phenylpropanoid and lipid metabolism. The study applied recently developed GC-MS metabolomics methods and demonstrated their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production.
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Affiliation(s)
- Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, DK-1958, Denmark.
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, DK-1871, Denmark.
| | - Morten Arendt Rasmussen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, DK-1958, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Gentofte Hospital, Copenhagen, Denmark
| | - Rubini Maya Kannangara
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, DK-1871, Denmark
| | - Birthe Møller Jespersen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, DK-1958, Denmark
| | - Lars Munck
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, DK-1958, Denmark
| | - Søren Balling Engelsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg, DK-1958, Denmark.
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Kumar R, Bohra A, Pandey AK, Pandey MK, Kumar A. Metabolomics for Plant Improvement: Status and Prospects. FRONTIERS IN PLANT SCIENCE 2017; 8:1302. [PMID: 28824660 PMCID: PMC5545584 DOI: 10.3389/fpls.2017.01302] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 05/12/2023]
Abstract
Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.
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Affiliation(s)
- Rakesh Kumar
- Department of Plant Sciences, University of Hyderabad (UoH)Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Arun K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU)Amarkantak, India
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42
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Tang W, Hazebroek J, Zhong C, Harp T, Vlahakis C, Baumhover B, Asiago V. Effect of Genetics, Environment, and Phenotype on the Metabolome of Maize Hybrids Using GC/MS and LC/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5215-5225. [PMID: 28574696 DOI: 10.1021/acs.jafc.7b00456] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We evaluated the variability of metabolites in various maize hybrids due to the effect of environment, genotype, phenotype as well as the interaction of the first two factors. We analyzed 480 forage and the same number of grain samples from 21 genetically diverse non-GM Pioneer brand maize hybrids, including some with drought tolerance and viral resistance phenotypes, grown at eight North American locations. As complementary platforms, both GC/MS and LC/MS were utilized to detect a wide diversity of metabolites. GC/MS revealed 166 and 137 metabolites in forage and grain samples, respectively, while LC/MS captured 1341 and 635 metabolites in forage and grain samples, respectively. Univariate and multivariate analyses were utilized to investigate the response of the maize metabolome to the environment, genotype, phenotype, and their interaction. Based on combined percentages from GC/MS and LC/MS datasets, the environment affected 36% to 84% of forage metabolites, while less than 7% were affected by genotype. The environment affected 12% to 90% of grain metabolites, whereas less than 27% were affected by genotype. Less than 10% and 11% of the metabolites were affected by phenotype in forage and grain, respectively. Unsupervised PCA and HCA analyses revealed similar trends, i.e., environmental effect was much stronger than genotype or phenotype effects. On the basis of comparisons of disease tolerant and disease susceptible hybrids, neither forage nor grain samples originating from different locations showed obvious phenotype effects. Our findings demonstrate that the combination of GC/MS and LC/MS based metabolite profiling followed by broad statistical analysis is an effective approach to identify the relative impact of environmental, genetic and phenotypic effects on the forage and grain composition of maize hybrids.
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Affiliation(s)
- Weijuan Tang
- Corporate Center for Analytical Sciences, DuPont Experimental Station , 200 Powder Mill Road, Wilmington, Delaware 19803, United States
| | - Jan Hazebroek
- Analytical & Genomics Technologies, DuPont Pioneer , 8325 NW 62nd Avenue, Johnston, Iowa 50131-7062, United States
| | - Cathy Zhong
- Global Regulatory Science, DuPont Experimental Station , 200 Powder Mill Road, Wilmington, Delaware 19803-0400, United States
| | - Teresa Harp
- Analytical & Genomics Technologies, DuPont Pioneer , 8325 NW 62nd Avenue, Johnston, Iowa 50131-7062, United States
| | - Chris Vlahakis
- Analytical & Genomics Technologies, DuPont Pioneer , 8325 NW 62nd Avenue, Johnston, Iowa 50131-7062, United States
| | - Brian Baumhover
- Global Regulatory Science, DuPont Pioneer , 8325 NW 62nd Avenue, Johnston, Iowa 50131-7060, United States
| | - Vincent Asiago
- Analytical & Genomics Technologies, DuPont Pioneer , 8325 NW 62nd Avenue, Johnston, Iowa 50131-7062, United States
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43
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Arpaia S, Birch ANE, Kiss J, van Loon JJA, Messéan A, Nuti M, Perry JN, Sweet JB, Tebbe CC. Assessing environmental impacts of genetically modified plants on non-target organisms: The relevance of in planta studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 583:123-132. [PMID: 28095991 DOI: 10.1016/j.scitotenv.2017.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 05/03/2023]
Abstract
In legal frameworks worldwide, genetically modified plants (GMPs) are subjected to pre-market environmental risk assessment (ERA) with the aim of identifying potential effects on the environment. In the European Union, the EFSA Guidance Document introduces the rationale that GMPs, as well as their newly produced metabolites, represent the potential stressor to be evaluated during ERA. As a consequence, during several phases of ERA for cultivation purposes, it is considered necessary to use whole plants or plant parts in experimental protocols. The importance of in planta studies as a strategy to address impacts of GMPs on non-target organisms is demonstrated, to evaluate both effects due to the intended modification in plant phenotype (e.g. expression of Cry proteins) and effects due to unintended modifications in plant phenotype resulting from the transformation process (e.g. due to somaclonal variations or pleiotropic effects). In planta tests are also necessary for GMPs in which newly expressed metabolites cannot easily be studied in vitro. This paper reviews the scientific literature supporting the choice of in planta studies as a fundamental tool in ERA of GMPs in cultivation dossiers; the evidence indicates they can realistically mimic the ecological relationships occurring in their receiving environments and provide important insights into the biology and sustainable management of GMPs.
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Affiliation(s)
| | | | - Jozsef Kiss
- Plant Protection Institute, Szent Istvan University, Gödöllö, Hungary
| | - Joop J A van Loon
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
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Li R, Quan S, Yan X, Biswas S, Zhang D, Shi J. Molecular characterization of genetically-modified crops: Challenges and strategies. Biotechnol Adv 2017; 35:302-309. [DOI: 10.1016/j.biotechadv.2017.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/23/2022]
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45
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Mishra P, Singh S, Rathinam M, Nandiganti M, Ram Kumar N, Thangaraj A, Thimmegowda V, Krishnan V, Mishra V, Jain N, Rai V, Pattanayak D, Sreevathsa R. Comparative Proteomic and Nutritional Composition Analysis of Independent Transgenic Pigeon Pea Seeds Harboring cry1AcF and cry2Aa Genes and Their Nontransgenic Counterparts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1395-1400. [PMID: 28114755 DOI: 10.1021/acs.jafc.6b05301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Safety assessment of genetically modified plants is an important aspect prior to deregulation. Demonstration of substantial equivalence of the transgenics compared to their nontransgenic counterparts can be performed using different techniques at various molecular levels. The present study is a first-ever comprehensive evaluation of pigeon pea transgenics harboring two independent cry genes, cry2Aa and cry1AcF. The absence of unintended effects in the transgenic seed components was demonstrated by proteome and nutritional composition profiling. Analysis revealed that no significant differences were found in the various nutritional compositional analyses performed. Additionally, 2-DGE-based proteome analysis of the transgenic and nontransgenic seed protein revealed that there were no major changes in the protein profile, although a minor fold change in the expression of a few proteins was observed. Furthermore, the study also demonstrated that neither the integration of T-DNA nor the expression of the cry genes resulted in the production of unintended effects in the form of new toxins or allergens.
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Affiliation(s)
- Pragya Mishra
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Shweta Singh
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Maniraj Rathinam
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | | | - Nikhil Ram Kumar
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | | | - Vinutha Thimmegowda
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute , New Delhi 110012, India
| | - Veda Krishnan
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute , New Delhi 110012, India
| | - Vagish Mishra
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Neha Jain
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Vandna Rai
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Debasis Pattanayak
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Research Centre on Plant Biotechnology , New Delhi 110012, India
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Mesnage R, Agapito-Tenfen SZ, Vilperte V, Renney G, Ward M, Séralini GE, Nodari RO, Antoniou MN. An integrated multi-omics analysis of the NK603 Roundup-tolerant GM maize reveals metabolism disturbances caused by the transformation process. Sci Rep 2016; 6:37855. [PMID: 27991589 PMCID: PMC5171704 DOI: 10.1038/srep37855] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Glyphosate tolerant genetically modified (GM) maize NK603 was assessed as 'substantially equivalent' to its isogenic counterpart by a nutrient composition analysis in order to be granted market approval. We have applied contemporary in depth molecular profiling methods of NK603 maize kernels (sprayed or unsprayed with Roundup) and the isogenic corn to reassess its substantial equivalence status. Proteome profiles of the maize kernels revealed alterations in the levels of enzymes of glycolysis and TCA cycle pathways, which were reflective of an imbalance in energy metabolism. Changes in proteins and metabolites of glutathione metabolism were indicative of increased oxidative stress. The most pronounced metabolome differences between NK603 and its isogenic counterpart consisted of an increase in polyamines including N-acetyl-cadaverine (2.9-fold), N-acetylputrescine (1.8-fold), putrescine (2.7-fold) and cadaverine (28-fold), which depending on context can be either protective or a cause of toxicity. Our molecular profiling results show that NK603 and its isogenic control are not substantially equivalent.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King’s College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | | | - Vinicius Vilperte
- CropScience Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, Brazil
| | - George Renney
- Proteomics Facility, King’s College London, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | - Malcolm Ward
- Proteomics Facility, King’s College London, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | - Gilles-Eric Séralini
- University of Caen, Institute of Biology, EA 2608 and Network on Risks, Quality and Sustainable Environment, MRSH, Esplanade de la Paix, University of Caen, Caen 14032, Cedex, France
| | - Rubens O. Nodari
- CropScience Department, Federal University of Santa Catarina, Rod. Admar Gonzaga 1346, 88034-000 Florianópolis, Brazil
| | - Michael N. Antoniou
- Gene Expression and Therapy Group, King’s College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
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47
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Zhang C, Wohlhueter R, Zhang H. Genetically modified foods: A critical review of their promise and problems. FOOD SCIENCE AND HUMAN WELLNESS 2016. [DOI: 10.1016/j.fshw.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Pasoreck EK, Su J, Silverman IM, Gosai SJ, Gregory BD, Yuan JS, Daniell H. Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1862-75. [PMID: 27507797 PMCID: PMC4980996 DOI: 10.1111/pbi.12548] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 05/09/2023]
Abstract
The impact of metabolic engineering on nontarget pathways and outcomes of metabolic engineering from different genomes are poorly understood questions. Therefore, squalene biosynthesis genes FARNESYL DIPHOSPHATE SYNTHASE (FPS) and SQUALENE SYNTHASE (SQS) were engineered via the Nicotiana tabacum chloroplast (C), nuclear (N) or both (CN) genomes to promote squalene biosynthesis. SQS levels were ~4300-fold higher in C and CN lines than in N, but all accumulated ~150-fold higher squalene due to substrate or storage limitations. Abnormal leaf and flower phenotypes, including lower pollen production and reduced fertility, were observed regardless of the compartment or level of transgene expression. Substantial changes in metabolomes of all lines were observed: levels of 65-120 unrelated metabolites, including the toxic alkaloid nicotine, changed by as much as 32-fold. Profound effects of transgenesis on nontarget gene expression included changes in the abundance of 19 076 transcripts by up to 2000-fold in CN; 7784 transcripts by up to 1400-fold in N; and 5224 transcripts by as much as 2200-fold in C. Transporter-related transcripts were induced, and cell cycle-associated transcripts were disproportionally repressed in all three lines. Transcriptome changes were validated by qRT-PCR. The mechanism underlying these large changes likely involves metabolite-mediated anterograde and/or retrograde signalling irrespective of the level of transgene expression or end product, due to imbalance of metabolic pools, offering new insight into both anticipated and unanticipated consequences of metabolic engineering.
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Affiliation(s)
- Elise K Pasoreck
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jin Su
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian M Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Sager J Gosai
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua S Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Henry Daniell
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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49
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Qi X, Liu B, Song Q, Zou B, Bu Y, Wu H, Ding L, Zhou G. Assessing Fungal Population in Soil Planted with Cry1Ac and CPTI Transgenic Cotton and Its Conventional Parental Line Using 18S and ITS rDNA Sequences over Four Seasons. FRONTIERS IN PLANT SCIENCE 2016; 7:1023. [PMID: 27462344 PMCID: PMC4940383 DOI: 10.3389/fpls.2016.01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/28/2016] [Indexed: 05/26/2023]
Abstract
Long-term growth of genetically modified plants (GMPs) has raised concerns regarding their ecological effects. Here, FLX-pyrosequencing of region I (18S) and region II (ITS1, 5.8S, and ITS2) rDNA was used to characterize fungal communities in soil samples after 10-year monoculture of one representative transgenic cotton line (TC-10) and 15-year plantation of various transgenic cotton cultivars (TC-15mix) over four seasons. Soil fungal communities in the rhizosphere of non-transgenic control (CC) were also compared. No notable differences were observed in soil fertility variables among CC, TC-10, and TC-15mix. Within seasons, the different estimations were statistically indistinguishable. There were 411 and 2 067 fungal operational taxonomic units in the two regions, respectively. More than 75% of fungal taxa were stable in both CC and TC except for individual taxa with significantly different abundance between TC and CC. Statistical analysis revealed no significant differences between CC and TC-10, while discrimination of separating TC-15mix from CC and TC-10 with 37.86% explained variance in PCoA and a significant difference of Shannon indexes between TC-10 and TC-15mix were observed in region II. As TC-15mix planted with a mixture of transgenic cottons (Zhongmian-29, 30, and 33B) for over 5 years, different genetic modifications may introduce variations in fungal diversity. Further clarification is necessary by detecting the fungal dynamic changes in sites planted in monoculture of various transgenic cottons. Overall, we conclude that monoculture of one representative transgenic cotton cultivar may have no effect on fungal diversity compared with conventional cotton. Furthermore, the choice of amplified region and methodology has potential to affect the outcome of the comparison between GM-crop and its parental line.
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Affiliation(s)
- Xiemin Qi
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing UniversityNanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical UniversityNanjing, China
| | - Biao Liu
- Key Laboratory of Biosafety, Ministry of Environmental Protection of China, Nanjing Institute of Environmental SciencesNanjing, China
| | - Qinxin Song
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing UniversityNanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical UniversityNanjing, China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing UniversityNanjing, China
| | - Ying Bu
- Huadong Research Institute for Medicine and BiotechnicsNanjing, China
| | - Haiping Wu
- Huadong Research Institute for Medicine and BiotechnicsNanjing, China
| | - Li Ding
- Department of Pharmaceutical Analysis, China Pharmaceutical UniversityNanjing, China
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, School of Medicine, Nanjing UniversityNanjing, China
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50
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Khan MS, Khan MA, Ahmad D. Assessing Utilization and Environmental Risks of Important Genes in Plant Abiotic Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2016; 7:792. [PMID: 27446095 PMCID: PMC4919908 DOI: 10.3389/fpls.2016.00792] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/22/2016] [Indexed: 05/22/2023]
Abstract
Transgenic plants with improved salt and drought stress tolerance have been developed with a large number of abiotic stress-related genes. Among these, the most extensively used genes are the glycine betaine biosynthetic codA, the DREB transcription factors, and vacuolar membrane Na(+)/H(+) antiporters. The use of codA, DREBs, and Na(+)/H(+) antiporters in transgenic plants has conferred stress tolerance and improved plant phenotype. However, the future deployment and commercialization of these plants depend on their safety to the environment. Addressing environmental risk assessment is challenging since mechanisms governing abiotic stress tolerance are much more complex than that of insect resistance and herbicide tolerance traits, which have been considered to date. Therefore, questions arise, whether abiotic stress tolerance genes need additional considerations and new measurements in risk assessment and, whether these genes would have effects on weediness and invasiveness potential of transgenic plants? While considering these concerns, the environmental risk assessment of abiotic stress tolerance genes would need to focus on the magnitude of stress tolerance, plant phenotype and characteristics of the potential receiving environment. In the present review, we discuss environmental concerns and likelihood of concerns associated with the use of abiotic stress tolerance genes. Based on our analysis, we conclude that the uses of these genes in domesticated crop plants are safe for the environment. Risk assessment, however, should be carefully conducted on biofeedstocks and perennial plants taking into account plant phenotype and the potential receiving environment.
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Affiliation(s)
- Mohammad S. Khan
- Faculty of Crop Production Sciences, Institute of Biotechnology and Genetic Engineering, The University of Agriculture, PeshawarPakistan
| | - Muhammad A. Khan
- Research School of Biology, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACTAustralia
| | - Dawood Ahmad
- Faculty of Crop Production Sciences, Institute of Biotechnology and Genetic Engineering, The University of Agriculture, PeshawarPakistan
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