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Wang X, Niu S, Yang J, Dong Y, Liu X, Jiao Y, Wang Z. Effects of stacking breeding on the methylome and transcriptome profile of transgenic rice with glyphosate tolerance. PLANTA 2023; 258:34. [PMID: 37378818 DOI: 10.1007/s00425-023-04181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
MAIN CONCLUSION Transcriptomics and methylomics were used to identify the potential effects resulting from GM rice breeding stacks, which provided scientific data for the safety assessment strategy of stacked GM crops in China. Gene interaction is one of the main concerns for stacked genetically modified crop safety. With the development of technology, the combination of omics and bioinformatics has become a useful tool to evaluate the unintended effects of genetically modified crops. In this study, transcriptomics and methylomics were used as molecular profiling techniques to identify the potential effects of stack through breeding. Stacked transgenic rice En-12 × Ec-26 was used as material, which was obtained through hybridization using parents En-12 and Ec-26, in which the foreign protein can form functional EPSPS protein by intein-mediated trans-splitting. Differentially methylated region (DMR) analysis showed that the effect of stacking breeding on methylation was less than that of genetic transformation at the methylome level. Differentially expressed gene (DEG) analysis showed that the DEGs between En-12 × Ec-26 and its parents were far fewer than those between transgenic rice and Zhonghua 11 (ZH11), and no unintended new genes were found in En-12 × Ec-26. Statistical analysis of gene expression and methylation involved in shikimic acid metabolism showed that there was no difference in gene expression, although there were 16 and 10 DMR genes between En-12 × Ec-26 and its parents (En and Ec) in methylation, respectively. The results indicated that the effect of stacking breeding on gene expression and DNA methylation was less than the effect of genetic transformation. This study provides scientific data supporting safety assessments of stacked GM crops in China.
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Affiliation(s)
- Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Shance Niu
- College of Horticulture, Hebei Agricultural University, Baoding, 071001, China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jiangtao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Yufeng Dong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Cropedit Biotechnology Co., Ltd, Beijing, 102206, China
| | - Xiaojing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China
| | - Yue Jiao
- Development Center for Science and Technology, MARA, Beijing, 100122, China.
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Key Laboratory on Molecular Safety Assessment of Agri-GMO, MARA, Beijing, 100081, China.
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Wang X, Zhang X, Yang J, Liu X, Song Y, Wang Z. Genetic variation assessment of stacked-trait transgenic maize via conventional breeding. BMC PLANT BIOLOGY 2019; 19:346. [PMID: 31391002 PMCID: PMC6686426 DOI: 10.1186/s12870-019-1956-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The safety assessment and control of stacked transgenic crops is increasingly important due to continuous crop development and is urgently needed in China. The genetic stability of foreign genes and unintended effects are the primary problems encountered in safety assessment. Omics techniques are useful for addressing these problems. The stacked transgenic maize variety 12-5 × IE034, which has insect-resistant and glyphosate-tolerant traits, was developed via a breeding stack using 12-5 and IE034 as parents. Using 12-5 × IE034, its parents (12-5 and IE034), and different maize varieties as materials, we performed proteomic profiling, molecular characterization and a genetic stability analysis. RESULTS Our results showed that the copy number of foreign genes in 12-5 × IE034 is identical to that of its parents 12-5 and IE034. Foreign genes can be stably inherited over different generations. Proteomic profiling analysis found no newly expressed proteins in 12-5 × IE034, and the differences in protein expression between 12 and 5 × IE034 and its parents were within the range of variation of conventional maize varieties. The expression levels of key enzymes participating in the shikimic acid pathway which is related to glyphosate tolerance of 12-5 × IE034 were not significantly different from those of its parents or five conventional maize varieties, which indicated that without selective pressure by glyphosate, the introduced EPSPS synthase is not has a pronounced impact on the synthesis of aromatic amino acids in maize. CONCLUSIONS Stacked-trait development via conventional breeding did not have an impact on the genetic stability of T-DNA, and the impact of stacked breeding on the maize proteome was less significant than that of genotypic differences. The results of this study provide a theoretical basis for the development of a safety assessment approach for stacked-trait transgenic crops in China.
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Affiliation(s)
- Xujing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xin Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Jiangtao Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Xiaojing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Yaya Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
| | - Zhixing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, MARA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, 12 Zhuangguancun South Street, Beijing, 100081 China
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3
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Concolino A, Olivo E, Tammè L, Fiumara CV, De Angelis MT, Quaresima B, Agosti V, Costanzo FS, Cuda G, Scumaci D. Proteomics Analysis to Assess the Role of Mitochondria in BRCA1-Mediated Breast Tumorigenesis. Proteomes 2018; 6:proteomes6020016. [PMID: 29584711 PMCID: PMC6027205 DOI: 10.3390/proteomes6020016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/21/2022] Open
Abstract
Mitochondria are the organelles deputed to energy production, but they are also involved in carcinogenesis, cancer progression, and metastasis, playing a role in altered energy metabolism in cancer cells. Mitochondrial metabolism is connected with several mitochondrial pathways such as ROS signaling, Ca2+ homeostasis, mitophagy, and mitochondrial biogenesis. These pathways are merged in an interactive super-network that seems to play a crucial role in cancer. Germline mutations of the BRCA1 gene account for 5–10% of breast cancers and confer a risk of developing the disease 10- to 20-fold much higher than in non-carriers. By considering metabolic networks that could reconcile both genetic and non-genetic causal mechanisms in BRCA1 driven tumorigenesis, we herein based our study on the hypothesis that BRCA1 haploinsufficiency might drive metabolic rewiring in breast epithelial cells, acting as a push toward malignant transformation. Using 2D-DIGE we analyzed and compared the mitochondrial proteomic profile of sporadic breast cancer cell line (MCF7) and BRCA1 mutated breast cancer cell line (HCC1937). Image analysis was carried out with Decider Software, and proteins differentially expressed were identified by LC-MS/MS on a quadrupole-orbitrap mass spectrometer Q-Exactive. Ingenuity pathways analysis software was used to analyze the fifty-three mitochondrial proteins whose expression resulted significantly altered in response to BRCA1 mutation status. Mitochondrial Dysfunction and oxidative phosphorylation, and energy production and nucleic acid metabolism were, respectively, the canonical pathway and the molecular function mainly affected. Western blotting analysis was done to validate the expression and the peculiar mitochondrial compartmentalization of specific proteins such us HSP60 and HIF-1α. Particularly intriguing is the correlation between BRCA1 mutation status and HIF-1α localization into the mitochondria in a BRCA1 dependent manner. Data obtained led us to hypothesize an interesting connection between BRCA1 and mitochondria pathways, capable to trigger metabolic changes, which, in turn, sustain the high energetic and anabolic requirements of the malignant phenotype.
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Affiliation(s)
- Antonio Concolino
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
| | - Erika Olivo
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
| | - Laura Tammè
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
| | - Claudia Vincenza Fiumara
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
| | - Maria Teresa De Angelis
- Stem Cell Laboratory, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Salvatore Venuta University Campus, Catanzaro 88100, Italy.
| | - Barbara Quaresima
- Laboratory of Molecular Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro 88100, Italy.
- CIS for Genomics and Molecular Pathology, Magna Graecia University of Catanzaro, Catanzaro 88100, Italy.
| | - Valter Agosti
- Laboratory of Molecular Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro 88100, Italy.
- CIS for Genomics and Molecular Pathology, Magna Graecia University of Catanzaro, Catanzaro 88100, Italy.
| | - Francesco Saverio Costanzo
- Laboratory of Molecular Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro 88100, Italy.
- CIS for Genomics and Molecular Pathology, Magna Graecia University of Catanzaro, Catanzaro 88100, Italy.
| | - Giovanni Cuda
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
| | - Domenica Scumaci
- Laboratory of Proteomics, Research Center of Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, Catanzaro 88100, Italy.
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Daddiego L, Bianco L, Capodicasa C, Carbone F, Dalmastri C, Daroda L, Del Fiore A, De Rossi P, Di Carli M, Donini M, Lopez L, Mengoni A, Paganin P, Perrotta G, Bevivino A. Omics approaches on fresh-cut lettuce reveal global molecular responses to sodium hypochlorite and peracetic acid treatment. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:737-750. [PMID: 28675480 DOI: 10.1002/jsfa.8521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Lettuce is a leafy vegetable that is extensively commercialized as a ready-to-eat product because of its widespread use in human nutrition as salad. It is well known that washing treatments can severely affect the quality and shelf-life of ready-to-eat vegetables. The study presented here evaluated the effect of two washing procedures on fresh-cut lettuce during storage. RESULTS An omics approach was applied to reveal global changes at molecular level induced by peracetic acid washing in comparison with sodium hypochlorite treatment. Microbiological analyses were also performed to quantify total bacterial abundance and composition. The study revealed wide metabolic alterations induced by the two sanitizers. In particular, transcriptomic and proteomic analyses pointed out a number of transcripts and proteins differentially accumulated in response to peracetic acid washing, mainly occurring on the first day of storage. In parallel, different microbiota composition and significant reduction in total bacterial load following washing were also observed. CONCLUSION The results provide useful information for the fresh-cut industry to select an appropriate washing procedure preserving fresh-like attributes as much as possible during storage of the end product. Molecular evidence indicated peracetic acid to be a valid alternative to sodium hypochlorite as sanitizer solution. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Linda Bianco
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Cristina Capodicasa
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Fabrizio Carbone
- Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Citrus and Tree Fruit, Rende, (CS), Italy
| | - Claudia Dalmastri
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Lorenza Daroda
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Antonella Del Fiore
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Patrizia De Rossi
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Mariasole Di Carli
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Marcello Donini
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loredana Lopez
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Paganin
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Gaetano Perrotta
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Trisaia Research Center, Rotondella, MT, Italy
| | - Annamaria Bevivino
- Department of Sustainability and Productivity of Territorial Systems, Biotechnology and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
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5
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Villani ME, Massa S, Lopresto V, Pinto R, Salzano AM, Scaloni A, Benvenuto E, Desiderio A. Effects of high-intensity static magnetic fields on a root-based bioreactor system for space applications. LIFE SCIENCES IN SPACE RESEARCH 2017; 15:79-87. [PMID: 29198317 DOI: 10.1016/j.lssr.2017.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
Static magnetic fields created by superconducting magnets have been proposed as an effective solution to protect spacecrafts and planetary stations from cosmic radiations. This shield can deflect high-energy particles exerting injurious effects on living organisms, including plants. In fact, plant systems are becoming increasingly interesting for space adaptation studies, being useful not only as food source but also as sink of bioactive molecules in future bioregenerative life-support systems (BLSS). However, the application of protective magnetic shields would generate inside space habitats residual magnetic fields, of the order of few hundreds milli Tesla, whose effect on plant systems is poorly known. To simulate the exposure conditions of these residual magnetic fields in shielded environment, devices generating high-intensity static magnetic field (SMF) were comparatively evaluated in blind exposure experiments (250 mT, 500 mT and sham -no SMF-). The effects of these SMFs were assayed on tomato cultures (hairy roots) previously engineered to produce anthocyanins, known for their anti-oxidant properties and possibly useful in the setting of BLSS. Hairy roots exposed for periods ranging from 24 h to 11 days were morphometrically analyzed to measure their growth and corresponding molecular changes were assessed by a differential proteomic approach. After disclosing blind exposure protocol, a stringent statistical elaboration revealed the absence of significant differences in the soluble proteome, perfectly matching phenotypic results. These experimental evidences demonstrate that the identified plant system well tolerates the exposure to these magnetic fields. Results hereby described reinforce the notion of using this plant organ culture as a tool in ground-based experiments simulating space and planetary environments, in a perspective of using tomato 'hairy root' cultures as bioreactor of ready-to-use bioactive molecules during future long-term space missions.
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Affiliation(s)
- Maria Elena Villani
- ENEA - National Agency for Energy, New Technologies and Sustainable Economic Development, Casaccia Research Center, Biotechnology and Agro-Industry Division, Via Anguillarese 301, Rome 00123, Italy
| | - Silvia Massa
- ENEA - National Agency for Energy, New Technologies and Sustainable Economic Development, Casaccia Research Center, Biotechnology and Agro-Industry Division, Via Anguillarese 301, Rome 00123, Italy
| | - Vanni Lopresto
- ENEA, Casaccia Research Center, Health Protection Technologies Division, Via Anguillarese 301, Rome 00123, Italy
| | - Rosanna Pinto
- ENEA, Casaccia Research Center, Health Protection Technologies Division, Via Anguillarese 301, Rome 00123, Italy
| | - Anna Maria Salzano
- CNR - National Research Council, ISPAAM, Proteomics & Mass Spectrometry Laboratory, Naples Italy
| | - Andrea Scaloni
- CNR - National Research Council, ISPAAM, Proteomics & Mass Spectrometry Laboratory, Naples Italy
| | - Eugenio Benvenuto
- ENEA - National Agency for Energy, New Technologies and Sustainable Economic Development, Casaccia Research Center, Biotechnology and Agro-Industry Division, Via Anguillarese 301, Rome 00123, Italy.
| | - Angiola Desiderio
- ENEA - National Agency for Energy, New Technologies and Sustainable Economic Development, Casaccia Research Center, Biotechnology and Agro-Industry Division, Via Anguillarese 301, Rome 00123, Italy.
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6
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Arena S, D'Ambrosio C, Vitale M, Mazzeo F, Mamone G, Di Stasio L, Maccaferri M, Curci PL, Sonnante G, Zambrano N, Scaloni A. Differential representation of albumins and globulins during grain development in durum wheat and its possible functional consequences. J Proteomics 2017; 162:86-98. [DOI: 10.1016/j.jprot.2017.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 01/03/2023]
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7
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Josić D, Peršurić Ž, Rešetar D, Martinović T, Saftić L, Kraljević Pavelić S. Use of Foodomics for Control of Food Processing and Assessing of Food Safety. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 81:187-229. [PMID: 28317605 DOI: 10.1016/bs.afnr.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.
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Affiliation(s)
- D Josić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia.
| | - Ž Peršurić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - D Rešetar
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - T Martinović
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - L Saftić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - S Kraljević Pavelić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
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8
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Liu Y, Zhang YX, Song SQ, Li J, Neal Stewart C, Wei W, Zhao Y, Wang WQ. A proteomic analysis of seeds from Bt-transgenic Brassica napus and hybrids with wild B. juncea. Sci Rep 2015; 5:15480. [PMID: 26486652 PMCID: PMC4614387 DOI: 10.1038/srep15480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Transgene insertions might have unintended side effects on the transgenic host, both crop and hybrids with wild relatives that harbor transgenes. We employed proteomic approaches to assess protein abundance changes in seeds from Bt-transgenic oilseed rape (Brassica napus) and its hybrids with wild mustard (B. juncea). A total of 24, 15 and 34 protein spots matching to 23, 13 and 31 unique genes were identified that changed at least 1.5 fold (p < 0.05, Student’s t-test) in abundance between transgenic (tBN) and non-transgenic (BN) oilseed rape, between hybrids of B. juncea (BJ) × tBN (BJtBN) and BJ × BN (BJBN) and between BJBN and BJ, respectively. Eight proteins had higher abundance in tBN than in BN. None of these proteins was toxic or nutritionally harmful to human health, which is not surprising since the seeds are not known to produce toxic proteins. Protein spots varying in abundance between BJtBN and BJBN seeds were the same or homologous to those in the respective parents. None of the differentially-accumulated proteins between BJtBN and BJBN were identical to those between tBN and BN. Results indicated that unintended effects resulted from transgene flow fell within the range of natural variability of hybridization and those found in the native host proteomes.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Ying-Xue Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475001, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yujie Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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9
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Park SH, Kim AY, Ma SH, Kim HM, Kang HS, Maeng JS, Ko K, Chung IS, Joung YH. Purification of human carcinoma antigen GA733-2 expressed inEscherichia coliand production of its polyclonal antibody in rabbit. Anim Cells Syst (Seoul) 2015. [DOI: 10.1080/19768354.2015.1030345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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10
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Masci S, Laino P, Janni M, Botticella E, Di Carli M, Benvenuto E, Danieli PP, Lilley KS, Lafiandra D, D'Ovidio R. Analysis of Quality-Related Parameters in Mature Kernels of Polygalacturonase Inhibiting Protein (PGIP) Transgenic Bread Wheat Infected with Fusarium graminearum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3962-3969. [PMID: 25823882 DOI: 10.1021/jf506003t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fusarium head blight, caused by the fungus Fusarium graminearum, has a detrimental effect on both productivity and qualitative properties of wheat. To evaluate its impact on wheat flour, we compared its effect on quality-related parameters between a transgenic bread wheat line expressing a bean polygalacturonase inhibiting protein (PGIP) and its control line. We have compared metabolic proteins, the amounts of gluten proteins and their relative ratios, starch content, yield, extent of pathogen contamination, and deoxynivalenol (DON) accumulation. These comparisons showed that Fusarium significantly decreases the amount of starch in infected control plants, but not in infected PGIP plants. The flour of PGIP plants contained also a lower amount of pathogen biomass and DON accumulation. Conversely, both gluten and metabolic proteins were not significantly influenced either by the transgene or by fungal infection. These results indicate that the transgenic PGIP expression reduces the level of infection, without changing significantly the wheat seed proteome and other quality-related parameters.
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Affiliation(s)
- Stefania Masci
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
| | - Paolo Laino
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
| | - Michela Janni
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
- ⊥Institute of Biosciences and BioResources (IBBR), CNR, Via G. Amendola 165/A, Bari, Italy
| | - Ermelinda Botticella
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
| | - Mariasole Di Carli
- §ENEA-Centro Ricerche Casaccia, Unità Tecnica BIORAD-FARM, via Anguillarese 301, 00123 Rome, Italy
| | - Eugenio Benvenuto
- §ENEA-Centro Ricerche Casaccia, Unità Tecnica BIORAD-FARM, via Anguillarese 301, 00123 Rome, Italy
| | - Pier Paolo Danieli
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
| | - Kathryn S Lilley
- #Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Domenico Lafiandra
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
| | - Renato D'Ovidio
- †Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia, University of Tuscia, Viterbo, Italy
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11
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Juarez P, Fernandez-del-Carmen A, Rambla JL, Presa S, Mico A, Granell A, Orzaez D. Evaluation of unintended effects in the composition of tomatoes expressing a human immunoglobulin A against rotavirus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:8158-8168. [PMID: 25065456 DOI: 10.1021/jf502292g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The production of neutralizing immunoglobulin A (IgA) in edible fruits as a means of oral passive immunization is a promising strategy for the inexpensive treatment of mucosal diseases. This approach is based on the assumption that the edible status remains unaltered in the immunoglobulin-expressing fruit, and therefore extensive purification is not required for mucosal delivery. However, unintended effects associated with IgA expression such as toxic secondary metabolites and protein allergens cannot be dismissed a priori and need to be investigated. This paper describes a collection of independent transgenic tomato lines expressing a neutralizing human IgA against rotavirus, a mucosal pathogen producing severe diarrhea episodes. This collection was used to evaluate possible unintended effects associated with recombinant IgA expression. A comparative analysis of protein and secondary metabolite profiles using wild type lines and other commercial varieties failed to find unsafe features significantly associated with IgA expression. Preliminary, the data indicate that formulations derived from IgA tomatoes are as safe for consumption as equivalent formulations derived from wild type tomatoes.
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MESH Headings
- Allergens/adverse effects
- Allergens/genetics
- Allergens/metabolism
- Antibodies, Neutralizing/adverse effects
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/metabolism
- Dietary Proteins/adverse effects
- Dietary Proteins/metabolism
- Food, Genetically Modified/adverse effects
- Fruit/adverse effects
- Fruit/chemistry
- Fruit/genetics
- Fruit/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Humans
- Immunization, Passive/adverse effects
- Immunoglobulin A/adverse effects
- Immunoglobulin A/genetics
- Immunoglobulin A/metabolism
- Least-Squares Analysis
- Solanum lycopersicum/adverse effects
- Solanum lycopersicum/chemistry
- Solanum lycopersicum/genetics
- Solanum lycopersicum/metabolism
- Plant Proteins/adverse effects
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/adverse effects
- Plants, Genetically Modified/chemistry
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Principal Component Analysis
- Recombinant Proteins/adverse effects
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Rotavirus/growth & development
- Rotavirus/immunology
- Rotavirus Infections/immunology
- Rotavirus Infections/prevention & control
- Rotavirus Infections/virology
- Secondary Metabolism
- Spain
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Affiliation(s)
- Paloma Juarez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientı́ficas, Universidad Politécnica de Valencia , Camino de Vera s/n, 46022 Valencia, Spain
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12
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Pobozy E, Sentkowska A, Piskor A. Comparison of three modifications of fused-silica capillaries and untreated capillaries for protein profiling of maize extracts by capillary electrophoresis. J Sep Sci 2014; 37:2388-94. [PMID: 24931305 DOI: 10.1002/jssc.201301236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 12/15/2022]
Abstract
In this work, capillary electrophoresis was applied to protein profiling of fractionated extracts of maize. A comparative study on the application of uncoated fused-silica capillaries and capillaries modified with hydroxypropylmethylcellulose, ω-iodoalkylammonium salt and a commercially available neutral capillary covalently coated with polyacrylamide is presented. The coating stability, background electrolyte composition, and separation efficiency were investigated. It was found that for zeins separation, the most stable and efficient was the capillary coated with polyacrylamide. Finally, the usefulness of these methods was studied for the differentiation of zein fraction in transgenic and nontransgenic maize. Zeins extracted from maize standards containing 0 and 5% m/m genetic modification were successfully separated, but slight differences were observed in terms of the zein content. Albumin and globulin fractions were analyzed with the use of unmodified fused-silica capillary with borate buffer pH 9 and the capillary coated with polyacrylamide with phosphate buffer pH 3. In the albumin fraction, additional peaks were found in genetically modified samples.
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Affiliation(s)
- Ewa Pobozy
- Department of Chemistry, Warsaw University, Warsaw, Poland
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13
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Valdés A, Simó C, Ibáñez C, García-Cañas V. Foodomics strategies for the analysis of transgenic foods. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Proteome changes induced by c-myb silencing in human chronic myeloid leukemia cells suggest molecular mechanisms and putative biomarkers of hematopoietic malignancies. J Proteomics 2013; 96:200-22. [PMID: 24220303 DOI: 10.1016/j.jprot.2013.10.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/18/2013] [Accepted: 10/30/2013] [Indexed: 11/23/2022]
Abstract
UNLABELLED To shed light on the molecular mechanisms associated with aberrant accumulation of c-Myb in chronic myeloid leukemia, comparative proteomic analysis was performed on c-myb RNAi-specifically silenced K562 cells, sampled on a time-course basis. 2D-DIGE technology highlighted 37 differentially-represented proteins that were further characterized by nLC-ESI-LIT-MS/MS and validated by western blotting and qRT-PCR analysis. Most of the deregulated proteins were related to protein folding, energy/primary metabolism, transcription/translation regulation and oxidative stress response. Protein network analysis suggested that glycolysis, gluconeogenesis and protein ubiquitination biosynthesis pathways were highly represented, confirming also the pivotal role of c-Myc. A specific reduced representation was observed for glyceraldehyde-3-phosphate-dehydrogenase and α-enolase, suggesting a possible role of c-Myb in the activation of aerobic glycolysis. A reduced amount was also observed for stress responsive heat shock 70kDa protein and 78kDa glucose-regulated protein, previously identified as direct targets of c-Myb. Among over-represented proteins, worth mentioning is the chromatin modifier chromobox protein homolog 3 that contributes to silencing of E2F- and Myc-responsive genes in quiescent G0 cells. Data here presented, while providing novel insights onto the molecular mechanisms underlying c-Myb activity, indicate potential protein biomarkers for monitoring the progression of chronic myeloid leukemia. BIOLOGICAL SIGNIFICANCE Myeloid leukemia is a malignant disease of the hematopoietic system in which cells of myeloid lineages accumulate to an undifferentiated state. In particular, it was shown that an aberrant accumulation of the c-Myb transcriptional factor is associated with the suppression of normal differentiation processes promoting the development of the hematopoietic malignancies. Many efforts have been recently made to identify novel genes directly targeted by c-Myb at a transcriptome level. In this work, we originally describe a differential proteomic approach to facilitate the comprehension of the regulation of the protein networks exerted by c-Myb. Our study reveals a complex network of proteins regulated by c-Myb. The functional heterogeneity of these proteins emphasizes the pleiotropic role of c-Myb as a regulator of genes that are crucial for energy production and stress response in leukemia. In fact, variations in glyceraldehyde-3-phosphate-dehydrogenase and α-enolase suggest a possible role of c-Myb in the activation of aerobic glycolysis. Moreover, significant differences were found for heat shock 70kDa protein and 78kDa glucose-regulated protein known as direct c-Myb targets. This work highlights potential protein biomarkers to look into disease progression and to develop translational medicine approaches in myeloid leukemia.
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15
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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16
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Gong CY, Wang T. Proteomic evaluation of genetically modified crops: current status and challenges. FRONTIERS IN PLANT SCIENCE 2013; 4:41. [PMID: 23471542 PMCID: PMC3590489 DOI: 10.3389/fpls.2013.00041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/19/2013] [Indexed: 05/07/2023]
Abstract
Hectares of genetically modified (GM) crops have increased exponentially since 1996, when such crops began to be commercialized. GM biotechnology, together with conventional breeding, has become the main approach to improving agronomic traits of crops. However, people are concerned about the safety of GM crops, especially GM-derived food and feed. Many efforts have been made to evaluate the unintended effects caused by the introduction of exogenous genes. "Omics" techniques have advantages over targeted analysis in evaluating such crops because of their use of high-throughput screening. Proteins are key players in gene function and are directly involved in metabolism and cellular development or have roles as toxins, antinutrients, or allergens, which are essential for human health. Thus, proteomics can be expected to become one of the most useful tools in safety assessment. This review assesses the potential of proteomics in evaluating various GM crops. We further describe the challenges in ensuring homogeneity and sensitivity in detection techniques.
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Affiliation(s)
| | - Tai Wang
- *Correspondence: Tai Wang, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Haidianqu, Beijing 100093, China. e-mail:
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17
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Mehrotra S, Goyal V. Evaluation of designer crops for biosafety--a scientist's perspective. Gene 2012; 515:241-8. [PMID: 23266812 DOI: 10.1016/j.gene.2012.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/26/2012] [Accepted: 12/04/2012] [Indexed: 01/16/2023]
Abstract
With the advent of transgenic technology, it has become possible to mobilize and express foreign genes into plants and to design crop varieties with better agronomic attributes and adaptability to challenging environmental conditions. Recent advances in transgenic technology have led to concerns about safety of transgenic crops to human and animal health and environment. Biosafety focuses on preventing, minimizing and eliminating risks associated with the research, production, and use of transgenic crops. Food biosafety involves studies of substantial equivalence related to compositional analysis, toxicity and allergenicity. Environmental biosafety involves glasshouse and field trials and study of unintended effects on non-target organisms. Transgenics are characterized at phenotypic and molecular levels for understanding the location of transgene insertion site, ploidy level, copy number, integrated vector sequences, protein expression and stability of the transgene. Various techniques employed for transgene characterization include flow cytometry, southern, northern and western analyses, real-time (qRT) PCR, competitive PCR, FISH, fiber-FISH, DNA micro-arrays, mRNA profiling, 2DE-MS, iTRAQ, FT-MS, NMR, GC-MS, CE-MS and biosensor-based approaches. Evaluation of transgene expression involves the application of integrated phenomics, transcriptomics, proteomics and metabolomics approaches. However, the relevance and application of these approaches may vary in different cases. The elaborate analysis of transgenic crops will facilitate the safety assessment and commercialization of transgenics and lead to global food security for the future.
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Affiliation(s)
- Shweta Mehrotra
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi-110012, India.
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18
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Yoshimatsu K, Kawano N, Kawahara N, Akiyama H, Teshima R, Nishijima M. [Current status in the commercialization and application of genetically modified plants and their effects on human and livestock health and phytoremediation]. YAKUGAKU ZASSHI 2012; 132:629-74. [PMID: 22687699 DOI: 10.1248/yakushi.132.629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Developments in the use of genetically modified plants for human and livestock health and phytoremediation were surveyed using information retrieved from Entrez PubMed, Chemical Abstracts Service, Google, congress abstracts and proceedings of related scientific societies, scientific journals, etc. Information obtained was classified into 8 categories according to the research objective and the usage of the transgenic plants as 1: nutraceuticals (functional foods), 2: oral vaccines, 3: edible curatives, 4: vaccine antigens, 5: therapeutic antibodies, 6: curatives, 7: diagnostic agents and reagents, and 8: phytoremediation. In total, 405 cases were collected from 2006 to 2010. The numbers of cases were 120 for nutraceuticals, 65 for oral vaccines, 25 for edible curatives, 36 for vaccine antigens, 36 for therapeutic antibodies, 76 for curatives, 15 for diagnostic agents and reagents, and 40 for phytoremediation (sum of each cases was 413 because some reports were related to several categories). Nutraceuticals, oral vaccines and curatives were predominant. The most frequently used edible crop was rice (51 cases), and tomato (28 cases), lettuce (22 cases), potato (18 cases), corn (15 cases) followed.
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Affiliation(s)
- Kayo Yoshimatsu
- Research Center for Medicinal Plant Resources, National Institute of Biomedical Innovation, Ibaraki, Japan.
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19
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Gong CY, Li Q, Yu HT, Wang Z, Wang T. Proteomics insight into the biological safety of transgenic modification of rice as compared with conventional genetic breeding and spontaneous genotypic variation. J Proteome Res 2012; 11:3019-29. [PMID: 22509807 DOI: 10.1021/pr300148w] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM indica rice, herbicide-resistant Bar68-1 carrying bar and insect-resistant 2036-1a carrying cry1Ac/sck, and their respective controls D68 and MH86, as well as indica variety MH63, a parental line for breeding MH86, and japonica variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between indica and japonica cultivars, second among indica varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating japonica and indica cultivars, as well as indica varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties.
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Affiliation(s)
- Chun Yan Gong
- Key Laboratory for Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing 100093, China
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20
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Falvo S, Di Carli M, Desiderio A, Benvenuto E, Moglia A, America T, Lanteri S, Acquadro A. 2-D DIGE analysis of UV-C radiation-responsive proteins in globe artichoke leaves. Proteomics 2012; 12:448-60. [PMID: 22162389 DOI: 10.1002/pmic.201100337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/22/2011] [Accepted: 11/24/2011] [Indexed: 01/08/2023]
Abstract
Plants respond to ultraviolet stress inducing a self-defence through the regulation of specific gene family members. The UV acclimation is the result of biochemical and physiological processes, such as enhancement of the antioxidant enzymatic system and accumulation of UV-absorbing phenolic compounds (e.g. flavonoids). Globe artichoke is an attractive species for studying the protein network involved in UV stress response, being characterized by remarkable levels of inducible antioxidants. Proteomic tools can assist the evaluation of the expression patterns of UV-responsive proteins and we applied the difference in-gel electrophoresis (DIGE) technology for monitoring the globe artichoke proteome variation at four time points following an acute UV-C exposure. A total of 145 UV-C-modulated proteins were observed and 119 were identified by LC-MS/MS using a ∼144,000 customized Compositae protein database, which included about 19,000 globe artichoke unigenes. Proteins were Gene Ontology (GO) categorized, visualized on their pathways and their behaviour was discussed. A predicted protein interaction network was produced and highly connected hub-like proteins were highlighted. Most of the proteins differentially modulated were chloroplast located, involved in photosynthesis, sugar metabolisms, protein folding and abiotic stress. The identification of UV-C-responsive proteins may contribute to shed light on the molecular mechanisms underlying plant responses to UV stress.
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Affiliation(s)
- Sara Falvo
- DIVAPRA, University of Turin, Grugliasco, Torino, Italy
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21
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Herrero M, Simó C, García-Cañas V, Ibáñez E, Cifuentes A. Foodomics: MS-based strategies in modern food science and nutrition. MASS SPECTROMETRY REVIEWS 2012; 31:49-69. [PMID: 21374694 DOI: 10.1002/mas.20335] [Citation(s) in RCA: 205] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/02/2011] [Accepted: 02/02/2011] [Indexed: 05/23/2023]
Abstract
Modern research in food science and nutrition is moving from classical methodologies to advanced analytical strategies in which MS-based techniques play a crucial role. In this context, Foodomics has been recently defined as a new discipline that studies food and nutrition domains through the application of advanced omics technologies in which MS techniques are considered indispensable. Applications of Foodomics include the genomic, transcriptomic, proteomic, and/or metabolomic study of foods for compound profiling, authenticity, and/or biomarker-detection related to food quality or safety; the development of new transgenic foods, food contaminants, and whole toxicity studies; new investigations on food bioactivity, food effects on human health, etc. This review work does not intend to provide an exhaustive revision of the many works published so far on food analysis using MS techniques. The aim of the present work is to provide an overview of the different MS-based strategies that have been (or can be) applied in the new field of Foodomics, discussing their advantages and drawbacks. Besides, some ideas about the foreseen development and applications of MS-techniques in this new discipline are also provided.
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Affiliation(s)
- Miguel Herrero
- Institute of Food Science Research (CIAL), CSIC, Nicolas Cabrera 9, Campus de Cantoblanco, 28049 Madrid, Spain
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22
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García-Cañas V, Simó C, León C, Ibáñez E, Cifuentes A. MS-based analytical methodologies to characterize genetically modified crops. MASS SPECTROMETRY REVIEWS 2011; 30:396-416. [PMID: 21500243 DOI: 10.1002/mas.20286] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/18/2009] [Accepted: 11/18/2009] [Indexed: 05/09/2023]
Abstract
The development of genetically modified crops has had a great impact on the agriculture and food industries. However, the development of any genetically modified organism (GMO) requires the application of analytical procedures to confirm the equivalence of the GMO compared to its isogenic non-transgenic counterpart. Moreover, the use of GMOs in foods and agriculture faces numerous criticisms from consumers and ecological organizations that have led some countries to regulate their production, growth, and commercialization. These regulations have brought about the need of new and more powerful analytical methods to face the complexity of this topic. In this regard, MS-based technologies are increasingly used for GMOs analysis to provide very useful information on GMO composition (e.g., metabolites, proteins). This review focuses on the MS-based analytical methodologies used to characterize genetically modified crops (also called transgenic crops). First, an overview on genetically modified crops development is provided, together with the main difficulties of their analysis. Next, the different MS-based analytical approaches applied to characterize GM crops are critically discussed, and include "-omics" approaches and target-based approaches. These methodologies allow the study of intended and unintended effects that result from the genetic transformation. This information is considered to be essential to corroborate (or not) the equivalence of the GM crop with its isogenic non-transgenic counterpart.
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Affiliation(s)
- Virginia García-Cañas
- Institute of Industrial Fermentations (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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23
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Kusano M, Fukushima A, Redestig H, Saito K. Metabolomic approaches toward understanding nitrogen metabolism in plants. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1439-53. [PMID: 21220784 DOI: 10.1093/jxb/erq417] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants can assimilate inorganic nitrogen (N) sources to organic N such as amino acids. N is the most important of the mineral nutrients required by plants and its metabolism is tightly coordinated with carbon (C) metabolism in the fundamental processes that permit plant growth. Increased understanding of N regulation may provide important insights for plant growth and improvement of quality of crops and vegetables because N as well as C metabolism are fundamental components of plant life. Metabolomics is a global biochemical approach useful to study N metabolism because metabolites not only reflect the ultimate phenotypes (traits), but can mediate transcript levels as well as protein levels directly and/or indirectly under different N conditions. This review outlines analytical and bioinformatic techniques particularly used to perform metabolomics for studying N metabolism in higher plants. Examples are used to illustrate the application of metabolomic techniques to the model plants Arabidopsis and rice, as well as other crops and vegetables.
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Affiliation(s)
- Miyako Kusano
- RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.
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24
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Wang X, Wang H, Wang D, Wang D, Han B, Tian W, Guo A. Thermal denaturation produced degenerative proteins and interfered with MS for proteins dissolved in lysis buffer in proteomic analysis. Electrophoresis 2011; 32:348-56. [DOI: 10.1002/elps.201000496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/20/2010] [Accepted: 11/30/2010] [Indexed: 11/06/2022]
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25
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Arruda SCC, Barbosa HDS, Azevedo RA, Arruda MAZ. Two-dimensional difference gel electrophoresis applied for analytical proteomics: fundamentals and applications to the study of plant proteomics. Analyst 2011; 136:4119-26. [DOI: 10.1039/c1an15513j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Di Carli M, Zamboni A, Pè ME, Pezzotti M, Lilley KS, Benvenuto E, Desiderio A. Two-dimensional differential in gel electrophoresis (2D-DIGE) analysis of grape berry proteome during postharvest withering. J Proteome Res 2010; 10:429-46. [PMID: 20945943 DOI: 10.1021/pr1005313] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The practice of postharvest withering is commonly used to correct quality traits and sugar concentration of high quality wines. To date, changes in the metabolome during the berry maturation process have been well documented; however, the biological events which occur at the protein level have yet to be fully investigated. To gain insight into the postharvest withering process, we studied the protein expression profiles of grape (Corvina variety) berry development focusing on withering utilizing a two-dimensional differential in gel electrophoresis (2D-DIGE) proteomics approach. Comparative analysis revealed changes in the abundance of numerous soluble proteins during the maturation and withering processes. On a total of 870 detected spots, 90 proteins were differentially expressed during berry ripening/withering and 72 were identified by MS/MS analysis. The majority of these proteins were related to stress and defense activity (30%), energy and primary metabolism (25%), cytoskeleton remodelling (7%), and secondary metabolism (5%). Moreover, this study demonstrates an active modulation of metabolic pathways throughout the slow dehydration process, including de novo protein synthesis in response to the stress condition and further evolution of physiological processes originated during ripening. These data represent an important insight into the withering process in terms of both Vitis germplasm characterization and knowledge which can assist quality improvement.
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Affiliation(s)
- Mariasole Di Carli
- Laboratorio Biotecnologie, UT BIORAD-FARM, ENEA Casaccia Research Centre, Rome, Italy.
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27
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Zamboni A, Di Carli M, Guzzo F, Stocchero M, Zenoni S, Ferrarini A, Tononi P, Toffali K, Desiderio A, Lilley KS, Pè ME, Benvenuto E, Delledonne M, Pezzotti M. Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks. PLANT PHYSIOLOGY 2010; 154:1439-59. [PMID: 20826702 PMCID: PMC2971619 DOI: 10.1104/pp.110.160275] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/08/2010] [Indexed: 05/19/2023]
Abstract
The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.
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Di Carli M, Villani ME, Bianco L, Lombardi R, Perrotta G, Benvenuto E, Donini M. Proteomic analysis of the plant-virus interaction in cucumber mosaic virus (CMV) resistant transgenic tomato. J Proteome Res 2010; 9:5684-97. [PMID: 20815412 DOI: 10.1021/pr100487x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cucumber mosaic virus (CMV), a member of the Cucumovirus genus, is the causal agent of several plant diseases in a wide range of host species, causing important economic losses in agriculture. Because of the lack of natural resistance genes in most crops, different genetic engineering strategies have been adopted to obtain virus-resistant plants. In a previous study, we described the engineering of transgenic tomato plants expressing a single-chain variable fragment antibody (scFv G4) that are specifically protected from CMV infection. In this work, we characterized the leaf proteome expressed during compatible plant-virus interaction in wild type and transgenic tomato. Protein changes in both inoculated and apical leaves were revealed using two-dimensional gel electrophoresis (2-DE) coupled to differential in gel electrophoresis (DIGE) technology. A total of 2084 spots were detected, and 50 differentially expressed proteins were identified by nanoscale liquid chromatographic-electrospray ionization-ion trap-tandem mass spectrometry (nLC-ESI-IT-MS/MS). The majority of these proteins were related to photosynthesis (38%), primary metabolism (18%), and defense activity (14%) and demonstrated to be actively down regulated by CMV in infected leaves. Moreover, our analysis revealed that asymptomatic apical leaves of transgenic inoculated plants had no protein profile alteration as compared to control wild type uninfected plants demonstrating that virus infection is confined to the inoculated leaves and systemic spread is hindered by the CMV coat protein (CP)-specific scFv G4 molecules. Our work is the first comparative study on compatible plant-virus interactions between engineered immunoprotected and susceptible wild type tomato plants, contributing to the understanding of antibody-mediated disease resistance mechanisms.
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Affiliation(s)
- Mariasole Di Carli
- ENEA, Centro Ricerche Casaccia, Via Anguillarese 301, I-00123, Rome, Italy.
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Scientific Opinion on the assessment of allergenicity of GM plants and microorganisms and derived food and feed. EFSA J 2010. [DOI: 10.2903/j.efsa.2010.1700] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Goulet C, Goulet C, Goulet MC, Michaud D. 2-DE proteome maps for the leaf apoplast of Nicotiana benthamiana. Proteomics 2010; 10:2536-44. [PMID: 20422621 DOI: 10.1002/pmic.200900382] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 04/08/2010] [Indexed: 12/19/2022]
Abstract
We provide 2-D gel reference maps for the apoplastic proteome of Nicotiana benthamiana leaves infiltrated or not with the bacterial gene vector Agrobacterium tumefaciens. About 90 proteins were analyzed by LC-MS/MS for identification and function assignment. We show, overall, an effective response of the plant to agroinfiltration involving a specific, cell wall maintenance-independent up-regulation of defense protein secretion. The proteome maps described should be a useful tool for systemic studies on plant-pathogen interactions or cell wall metabolism. They also should prove useful for the monitoring of secreted recombinant proteins and their possible pleiotropic effects along the cell secretory pathway of N. benthamiana leaves used as an expression platform for clinically useful proteins.
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Affiliation(s)
- Charles Goulet
- Département de phytologie, Université Laval, Québec QC, Canada
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31
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Brandão AR, Barbosa HS, Arruda MAZ. Image analysis of two-dimensional gel electrophoresis for comparative proteomics of transgenic and non-transgenic soybean seeds. J Proteomics 2010; 73:1433-40. [PMID: 20123049 DOI: 10.1016/j.jprot.2010.01.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 01/08/2010] [Accepted: 01/16/2010] [Indexed: 11/28/2022]
Abstract
Considering the importance of bidimensional electrophoresis and image analysis in comparative proteomics, the parameters that influence the analysis of protein expression of transgenic and non-transgenic soybean seeds were evaluated. The loaded mass of the proteins (150-500 microg), the pH separation range (3-10 or 4-7), and manual/automatic image editing were evaluated. Additionally, after optimizing the conditions, histograms and matchings were obtained in order to accurately analyze the variations (90%) in protein expression. From this, 10 proteins displayed significant differences in expression, and eight of them were characterized and identified by mass spectrometry.
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Affiliation(s)
- A R Brandão
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil
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Coll A, Nadal A, Collado R, Capellades G, Kubista M, Messeguer J, Pla M. Natural variation explains most transcriptomic changes among maize plants of MON810 and comparable non-GM varieties subjected to two N-fertilization farming practices. PLANT MOLECULAR BIOLOGY 2010; 73:349-62. [PMID: 20349115 DOI: 10.1007/s11103-010-9624-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 03/07/2010] [Indexed: 05/12/2023]
Abstract
The introduction of genetically modified organisms (GMO) in many countries follows strict regulations to ensure that only safety-tested products are marketed. Over the last few years, targeted approaches have been complemented by profiling methods to assess possible unintended effects of transformation. Here we used a commercial (Affymertix) microarray platform (i.e. allowing assessing the expression of approximately 1/3 of the genes of maize) to evaluate transcriptional differences between commercial MON810 GM maize and non-transgenic crops in real agricultural conditions, in a region where about 70% of the maize grown was MON810. To consider natural variation in gene expression in relation to biotech plants we took two common MON810/non-GM variety pairs as examples, and two farming practices (conventional and low-nitrogen fertilization). MON810 and comparable non-GM varieties grown in the field have very low numbers of sequences with differential expression, and their identity differs among varieties. Furthermore, we show that the differences between a given MON810 variety and the non-GM counterpart do not appear to depend to any major extent on the assayed cultural conditions, even though these differences may slightly vary between the conditions. In our study, natural variation explained most of the variability in gene expression among the samples. Up to 37.4% was dependent upon the variety (obtained by conventional breeding) and 31.9% a result of the fertilization treatment. In contrast, the MON810 GM character had a very minor effect (9.7%) on gene expression in the analyzed varieties and conditions, even though similar cryIA(b) expression levels were detected in the two MON810 varieties and nitrogen treatments. This indicates that transcriptional differences of conventionally-bred varieties and under different environmental conditions should be taken into account in safety assessment studies of GM plants.
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Affiliation(s)
- Anna Coll
- Institut de Tecnologia Agroalimentària (INTEA), Universitat de Girona, Campus Montilivi, EPS-I, Girona, Spain
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Acosta-Martin AE, Chwastyniak M, Beseme O, Drobecq H, Amouyel P, Pinet F. Impact of incomplete DNase I treatment on human macrophage proteome analysis. Proteomics Clin Appl 2009; 3:1236-46. [DOI: 10.1002/prca.200900113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 06/30/2009] [Accepted: 07/11/2009] [Indexed: 01/10/2023]
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