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Aggarwal B, Rajora N, Raturi G, Dhar H, Kadam SB, Mundada PS, Shivaraj SM, Varshney V, Deshmukh R, Barvkar VT, Salvi P, Sonah H. Biotechnology and urban agriculture: A partnership for the future sustainability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111903. [PMID: 37865210 DOI: 10.1016/j.plantsci.2023.111903] [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: 08/05/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
The global population is growing rapidly, and with it, the demand for food. In the coming decades, more and more people will be living in urban areas, where land for traditional agriculture is scarce. Urban agriculture can help to meet this growing demand for food in a sustainable way. Urban agriculture is the practice of growing food in urban areas. It can be done on rooftops, balconies, vacant lots, and even in alleyways. Urban agriculture can produce a variety of crops, including fruits, vegetables, and herbs. It can also help to improve air quality, reduce stormwater runoff, and create jobs. Biotechnology can be used to improve the efficiency and sustainability of urban agriculture. Biotechnological tools can be used to develop crops that are resistant to pests and diseases, that are more tolerant of drought and heat, and that have higher yields. Biotechnology can also be used to improve the nutritional value of crops. This review article discusses the need for and importance of urban agriculture, biotechnology, and genome editing in meeting the growing demand for food in urban areas. It also discusses the potential of biotechnology to improve the sustainability of urban agriculture.
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Affiliation(s)
- Bharti Aggarwal
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nitika Rajora
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Gaurav Raturi
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Hena Dhar
- Department of Microbiology, School of Biosciences, RIMT University, Mandi Gobindgarh, India
| | - Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Pankaj S Mundada
- Department of Biotechnology, Yashavantrao Chavan Institute of Science, Satara, India
| | - S M Shivaraj
- National Agri-Food Biotechnology Institute (NABI), Mohali, India; Department of Science, Alliance University, Bengaluru, Karnataka, India
| | - Vishal Varshney
- Govt. Shaheed Gend Singh College, Charama, Chhattisgarh, India
| | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana (CUH), Mahendergarh, India
| | | | - Prafull Salvi
- National Agri-Food Biotechnology Institute (NABI), Mohali, India.
| | - Humira Sonah
- Department of Biotechnology, Central University of Haryana (CUH), Mahendergarh, India.
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Lokya V, Parmar S, Pandey AK, Sudini HK, Huai D, Ozias-Akins P, Foyer CH, Nwosu CV, Karpinska B, Baker A, Xu P, Liao B, Mir RR, Chen X, Guo B, Nguyen HT, Kumar R, Bera SK, Singam P, Kumar A, Varshney RK, Pandey MK. Prospects for developing allergen-depleted food crops. THE PLANT GENOME 2023; 16:e20375. [PMID: 37641460 DOI: 10.1002/tpg2.20375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 06/08/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
In addition to the challenge of meeting global demand for food production, there are increasing concerns about food safety and the need to protect consumer health from the negative effects of foodborne allergies. Certain bio-molecules (usually proteins) present in food can act as allergens that trigger unusual immunological reactions, with potentially life-threatening consequences. The relentless working lifestyles of the modern era often incorporate poor eating habits that include readymade prepackaged and processed foods, which contain additives such as peanuts, tree nuts, wheat, and soy-based products, rather than traditional home cooking. Of the predominant allergenic foods (soybean, wheat, fish, peanut, shellfish, tree nuts, eggs, and milk), peanuts (Arachis hypogaea) are the best characterized source of allergens, followed by tree nuts (Juglans regia, Prunus amygdalus, Corylus avellana, Carya illinoinensis, Anacardium occidentale, Pistacia vera, Bertholletia excels), wheat (Triticum aestivum), soybeans (Glycine max), and kidney beans (Phaseolus vulgaris). The prevalence of food allergies has risen significantly in recent years including chance of accidental exposure to such foods. In contrast, the standards of detection, diagnosis, and cure have not kept pace and unfortunately are often suboptimal. In this review, we mainly focus on the prevalence of allergies associated with peanut, tree nuts, wheat, soybean, and kidney bean, highlighting their physiological properties and functions as well as considering research directions for tailoring allergen gene expression. In particular, we discuss how recent advances in molecular breeding, genetic engineering, and genome editing can be used to develop potential low allergen food crops that protect consumer health.
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Affiliation(s)
- Vadthya Lokya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sejal Parmar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Arun K Pandey
- College of Life Science of China Jiliang University (CJLU), Hangzhou, China
| | - Hari K Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Peggy Ozias-Akins
- Horticulture Department, The University of Georgia Tifton Campus, Tifton, GA, USA
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
| | | | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
| | - Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Pei Xu
- College of Life Science of China Jiliang University (CJLU), Hangzhou, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory for Crops Genetic Improvement, Crops Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Baozhu Guo
- USDA-ARS, Crop Genetics and Breeding Research Unit, Tifton, GA, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA
| | - Rakesh Kumar
- Department of Life Sciences, Central University of Karnataka, Gulbarga, India
| | | | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Anirudh Kumar
- Central Tribal University of Andhra Pradesh, Vizianagaram, Andhra Pradesh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Qu G, Wang K, Mu J, Zhuo J, Wang X, Li S, Ye X, Li Y, Yan Y, Li X. Identifying cis-Acting Elements Associated with the High Activity and Endosperm Specificity of the Promoters of Genes Encoding Low-Molecular-Weight Glutenin Subunits in Common Wheat ( Triticum aestivum). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37919930 DOI: 10.1021/acs.jafc.3c04209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Low-molecular-weight glutenin subunits (LMW-GSs) associated with bread-baking quality and flour nutrient quality accumulate in endosperms of common wheat and related species. However, the mechanism underlying the expression regulation of genes encoding LMW-GSs has not been fully elucidated. In this study, we identified LMW-D2 and LMW-D7, which are highly and weakly expressed, respectively, via the analysis of RNA-sequencing data of Chinese Spring wheat and wheat transgenic lines transformed with 5' deletion promoter fragments and GUS fusion constructs. The 605-bp fragment upstream of the LMW-D2 start codon could drive high levels of GUS expression in the endosperm. The truncated endosperm box located at the -300 site resulted in the loss of LMW-D2 promoter activity, and a single-nucleotide polymorphism on the GCN4 motif was closely related to the expression of LMW-GSs. TCT and TGACG motifs, as well as the others located on the 5' distal end, might also be involved in the transcription regulation of LMW-GSs. In transgenic lines, fusion proteins of LMW-GS and GUS were deposited into protein bodies. Our findings provide new insights into the mechanism underlying the transcription regulation of LMW-GSs and will contribute to the development of wheat endosperm as a bioreactor for the production of nutraceuticals, antibodies, vaccines, and medicinal proteins.
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Affiliation(s)
- Ge Qu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Ke Wang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junyi Mu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Jiahui Zhuo
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xinyu Wang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Shasha Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xingguo Ye
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaxuan Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing 100048, China
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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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Li Q, Wang X, Sun Z, Wu Y, Malkodslo MM, Ge J, Jing Z, Zhou Q, Cai J, Zhong Y, Huang M, Jiang D. DNA methylation levels of TaP5CS and TaBADH are associated with enhanced tolerance to PEG-induced drought stress triggered by drought priming in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107769. [PMID: 37263071 DOI: 10.1016/j.plaphy.2023.107769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Drought priming is a promising strategy to enhance tolerance to recurred drought in wheat. However, the underlying mechanisms of priming-induced tolerance are far from clear. Here, three different priming intensities (P1D, P2D, P3D) and two varieties with different sensitivities to drought priming were used to investigate the effects and mechanisms of drought priming. Results showed light (P1D) or moderate (P2D) drought priming intensity induced positive effects for the drought sensitive variety (YM16), while high (P3D) priming intensity brought a negative impact on the plant drought resistant. For drought insensitive one (XM33), light priming intensity had no significant effect on tolerance to drought, while moderate or high intensity showed better priming effects. Moderate priming induced higher leaf water potential and also the osmolytes levels. Consistent with the proline and betaine, the related synthetic enzymatic activities, as well as the expression of TaP5CS and TaBADH were higher in P2D in YM16 and P3D in XM33. The contents of proline and betaine showed a positive correlation with activities of SOD, CAT, GR, AsA, and GSH contents, and a negative correlation with O2.-, H2O2, and MDA contents. Further analysis revealed CG demethylation of ATG-proximal regions in the promoter of TaP5CS and TaBADH were involved in promoting the synthesis of proline and betaine in primed plants. Collectively, these findings demonstrate drought priming effect was variety independent but depended on the priming severity, and demethylation of TaP5CS and TaBADH involved in the accumulation of osmolytes which contribute to the enhanced drought tolerance induced by priming.
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Affiliation(s)
- Qing Li
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Wang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhuangzhuang Sun
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yixin Wu
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Maguje Masa Malkodslo
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiakun Ge
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zihan Jing
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qin Zhou
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Cai
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingxin Zhong
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mei Huang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production, Key Laboratory of Crop Ecophysiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Xu JH, Irshad F, Yan Y, Li C. Loss of Function of the RRMF Domain in OsROS1a Causes Sterility in Rice (Oryza sativa L.). Int J Mol Sci 2022; 23:ijms231911349. [PMID: 36232648 PMCID: PMC9569698 DOI: 10.3390/ijms231911349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
For crop seed production, the development of anthers and male fertility are the main agronomic traits and key biological processes for flowering plants. Active DNA demethylation regulates many plant developmental processes and is ensured by 5-meC DNA glycosylase enzymes. To find out the role of OsROS1a, OsROS1a gene editing mutants were generated using the CRISPR/Cas9 system. The osros1a mutants had shrink spikelets, smaller anthers and pollen grains, and were not stained by iodine staining showing a significant reduction in total soluble sugar and starch contents as compared to wildtype (WT), which caused complete male sterility. Similarly, the expression of genes involved in pollen and anther development was decreased in osros1a mutants as compared to WT. Furthermore, bisulfite sequencing showed that the CG and CHG methylation of the OsPKS2 gene promoter was significantly increased in the osros1a mutant, which caused a reduced expression of OsPKS2 in osros1a mutants. DNA methylation of the TDR gene promoter was similar between WT and osros1a mutants, indicating that the DNA methylation effect by OsROS1a was gene specific. The expression of OsROS1a in the mutants was not changed, but it produced a frame-shift mutation to truncate the Pem-CXXC and RRMF domains. Combined with previous studies, our findings suggested that the RRMF domain in OsROS1a is the functional domain and loss of RRMF for OsROS1a causes sterility in rice.
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Affiliation(s)
- Jian-Hong Xu
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
- Correspondence: (J.-H.X.); (C.L.)
| | - Faiza Irshad
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Yan
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chao Li
- Zhejiang Key Laboratory of Crop Germplasm, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
- Correspondence: (J.-H.X.); (C.L.)
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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8
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Un Jan Contreras S, Gardner CM. Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops. J Appl Microbiol 2022; 133:2877-2892. [PMID: 35892194 DOI: 10.1111/jam.15741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause.
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Affiliation(s)
- Sandra Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
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9
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Petrova DV, Permyakova NV, Grin IR, Zharkov DO. Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L. Vavilovskii Zhurnal Genet Selektsii 2022; 26:341-348. [PMID: 35860677 PMCID: PMC9257373 DOI: 10.18699/vjgb-22-41] [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: 11/26/2021] [Revised: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 11/19/2022] Open
Abstract
One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulation of development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologues of DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied. Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1), which contains all main structural domains required for catalytic activity. Using homologous modeling, we have constructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix– hairpin–helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA, and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand. The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower efficiency, showing minimal activity in the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted in a global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein and other homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the status of epigenetic methylation and to control gene activity.
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Affiliation(s)
- D. V. Petrova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - N. V. Permyakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. R. Grin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - D. O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
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The Function of DNA Demethylase Gene ROS1a Null Mutant on Seed Development in Rice ( Oryza Sativa) Using the CRISPR/CAS9 System. Int J Mol Sci 2022; 23:ijms23126357. [PMID: 35742811 PMCID: PMC9223687 DOI: 10.3390/ijms23126357] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 02/05/2023] Open
Abstract
The endosperm is the main nutrient source in cereals for humans, as it is a highly specialized storage organ for starch, lipids, and proteins, and plays an essential role in seed growth and development. Active DNA demethylation regulates plant developmental processes and is ensured by cytosine methylation (5-meC) DNA glycosylase enzymes. To find out the role of OsROS1a in seed development, the null mutant of OsROS1a was generated using the CRISPR/Cas9 system. The null mutant of OsROS1a was stable and heritable, which affects the major agronomic traits, particularly in rice seeds. The null mutant of OsROS1a showed longer and narrower grains, and seeds were deformed containing an underdeveloped and less-starch-producing endosperm with slightly irregularly shaped embryos. In contrast to the transparent grains of the wild type, the grains of the null mutant of OsROS1a were slightly opaque and rounded starch granules, with uneven shapes, sizes, and surfaces. A total of 723 differential expression genes (DEGs) were detected in the null mutant of OsROS1a by RNA-Seq, of which 290 were downregulated and 433 were upregulated. The gene ontology (GO) terms with the top 20 enrichment factors were visualized for cellular components, biological processes, and molecular functions. The key genes that are enriched for these GO terms include starch synthesis genes (OsSSIIa and OsSSIIIa) and cellulose synthesis genes (CESA2, CESA3, CESA6, and CESA8). Genes encoding polysaccharides and glutelin were found to be downregulated in the mutant endosperm. The glutelins were further verified by SDS-PAGE, suggesting that glutelin genes could be involved in the null mutant of OsROS1a seed phenotype and OsROS1a could have the key role in the regulation of glutelins. Furthermore, 378 differentially alternative splicing (AS) genes were identified in the null mutant of OsROS1a, suggesting that the OsROS1a gene has an impact on AS events. Our findings indicated that the function on rice endosperm development in the null mutant of OsROS1a could be influenced through regulating gene expression and AS, which could provide the base to properly understand the molecular mechanism related to the OsROS1a gene in the regulation of rice seed development.
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Liu J, Wu MW, Liu CM. Cereal Endosperms: Development and Storage Product Accumulation. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:255-291. [PMID: 35226815 DOI: 10.1146/annurev-arplant-070221-024405] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.
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Affiliation(s)
- Jinxin Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
| | - Ming-Wei Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China;
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
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12
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Xu Q, Wu L, Luo Z, Zhang M, Lai J, Li L, Springer NM, Li Q. DNA demethylation affects imprinted gene expression in maize endosperm. Genome Biol 2022; 23:77. [PMID: 35264226 PMCID: PMC8905802 DOI: 10.1186/s13059-022-02641-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. Results We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. Conclusions Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.
Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02641-x.
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Affiliation(s)
- Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Leiming Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixiang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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13
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Wen N, Osorio CE, Brew-Appiah RAT, Mejías JH, Alam T, Kashyap S, Reinbothe S, Reinbothe C, Moehs CP, von Wettstein D, Rustgi S. Targeting Induced Local Lesions in the Wheat DEMETER and DRE2 Genes, Responsible for Transcriptional Derepression of Wheat Gluten Proteins in the Developing Endosperm. Front Nutr 2022; 9:847635. [PMID: 35308262 PMCID: PMC8928260 DOI: 10.3389/fnut.2022.847635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/28/2022] [Indexed: 01/05/2023] Open
Abstract
Wheat is a major source of energy and nutrition worldwide, but it is also a primary cause of frequent diet-induced health issues, specifically celiac disease, for which the only effective therapy so far is strict dietary abstinence from gluten-containing grains. Wheat gluten proteins are grouped into two major categories: high-molecular-weight glutenin subunits (HMWgs), vital for mixing and baking properties, and gliadins plus low-molecular-weight glutenin subunits (LMWgs) that contain the overwhelming majority of celiac-causing epitopes. We put forth a hypothesis that eliminating gliadins and LMWgs while retaining HMWgs might allow the development of reduced-immunogenicity wheat genotypes relevant to most gluten-sensitive individuals. This hypothesis stems from the knowledge that the molecular structures and regulatory mechanisms of the genes encoding the two groups of gluten proteins are quite different, and blocking one group's transcription, without affecting the other's, is possible. The genes for gliadins and LMWgs have to be de-methylated by 5-methylcytosine DNA glycosylase/lyase (DEMETER) and an iron-sulfur (Fe-S) cluster biogenesis enzyme (DRE2) early during endosperm development to permit their transcription. In this study, a TILLING (Targeting Induced Local Lesions IN Genomes) approach was undertaken to identify mutations in the homoeologous DEMETER (DME) and DRE2 genes in common and durum wheat. Lines with mutations in these genes were obtained that displayed reduced content of immunogenic gluten proteins while retaining essential baking properties. Although our data at first glance suggest new possibilities for treating celiac disease and are therefore of medical and agronomical interest, it also shows that inducing mutations in the DME and DRE2 genes analyzed here affected pollen viability and germination. Hence there is a need to develop other approaches in the future to overcome this undesired effect.
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Affiliation(s)
- Nuan Wen
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Claudia E. Osorio
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Rhoda A. T. Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Jaime H. Mejías
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Tariq Alam
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, United States
| | - Samneet Kashyap
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, United States
| | - Steffen Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes, Université Grenoble-Alpes, BP53F, Grenoble, France
| | - Christiane Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes, Université Grenoble-Alpes, BP53F, Grenoble, France
| | | | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, United States
- *Correspondence: Sachin Rustgi
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Zhou Z, Liu C, Qin M, Li W, Hou J, Shi X, Dai Z, Yao W, Tian B, Lei Z, Li Y, Wu Z. Promoter DNA hypermethylation of TaGli-γ-2.1 positively regulates gluten strength in bread wheat. J Adv Res 2022; 36:163-173. [PMID: 35127171 PMCID: PMC8799914 DOI: 10.1016/j.jare.2021.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 06/11/2021] [Accepted: 06/28/2021] [Indexed: 12/30/2022] Open
Abstract
TaGli-γ-2.1 belonged to a subgroup of γ-gliadin multigene family. TaGli-γ-2.1 was a negative regulatory factor in gluten strength. Methylation of pTaGli-γ-2.1 played a key role in regulating TaGli-γ-2.1 expression. Lower γ-gliadin content followed with hypermethylation of pTaGli-γ-2.1. Decreasing TaGli-γ-2.1 expression could be used to improve gluten strength in wheat breeding.
Introduction Gliadins are the major components of gluten proteins with vital roles on properties of end-use wheat product and health-relate quality of wheat. However, the function and regulation mechanisms of γ-gliadin genes remain unclear. Objectives Dissect the effect of DNA methylation in the promoter of γ-gliadin gene on its expression level and gluten strength of wheat. Methods The prokaryotic expression and reduction–oxidation reactions were performed to identify the effect of TaGli-γ-2.1 on dough strength. Bisulfite analysis and 5-Aza-2′-deoxycytidine treatment were used to verify the regulation of TaGli-γ-2.1 expression by pTaGli-γ-2.1 methylation. The content of gluten proteins composition was measured by RP-HPLC, and the gluten strength was measured by Gluten Index and Farinograph. Results TaGli-γ-2.1 was classified into a subgroup of γ-gliadin multigene family and was preferentially expressed in the later period of grain filling. Addition of TaGli-γ-2.1 protein fragment into strong gluten wheat flour significantly decreased the stability time. Hypermethylation of three CG loci of pTaGli-γ-2.1 conferred to lower TaGli-γ-2.1 expression. Treatment with 5-Aza-2′-deoxycytidine in seeds of strong gluten wheat varieties increased the expression levels of TaGli-γ-2.1. Furthermore, the accumulations of gliadin and γ-gliadin were significantly decreased in hypermethylated wheat varieties, corresponding with the increasing of gluten index and dough stability time. Conclusion Epigenetic modification of pTaGli-γ-2.1 affected gluten strength by modulating the proportion of gluten proteins. Hypermethylation of pTaGli-γ-2.1 is a novel genetic resource for enhancing gluten strength in wheat quality breeding.
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Affiliation(s)
- Zhengfu Zhou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Agronomy College, Zhengzhou University, Zhengzhou 450001, China
| | - Congcong Liu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Maomao Qin
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenxu Li
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jinna Hou
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xia Shi
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ziju Dai
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Baoming Tian
- Agronomy College, Zhengzhou University, Zhengzhou 450001, China
| | - Zhensheng Lei
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- Agronomy College, Zhengzhou University, Zhengzhou 450001, China
| | - Yang Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhengqing Wu
- Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Agronomy College, Zhengzhou University, Zhengzhou 450001, China
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15
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Peng Y, Zhao Y, Yu Z, Zeng J, Xu D, Dong J, Ma W. Wheat Quality Formation and Its Regulatory Mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:834654. [PMID: 35432421 PMCID: PMC9006054 DOI: 10.3389/fpls.2022.834654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/09/2022] [Indexed: 05/07/2023]
Abstract
Elucidation of the composition, functional characteristics, and formation mechanism of wheat quality is critical for the sustainable development of wheat industry. It is well documented that wheat processing quality is largely determined by its seed storage proteins including glutenins and gliadins, which confer wheat dough with unique rheological properties, making it possible to produce a series of foods for human consumption. The proportion of different gluten components has become an important target for wheat quality improvement. In many cases, the processing quality of wheat is closely associated with the nutritional value and healthy effect of the end-products. The components of wheat seed storage proteins can greatly influence wheat quality and some can even cause intestinal inflammatory diseases or allergy in humans. Genetic and environmental factors have great impacts on seed storage protein synthesis and accumulation, and fertilization and irrigation strategies also greatly affect the seed storage protein content and composition, which together determine the final end-use quality of wheat. This review summarizes the recent progress in research on the composition, function, biosynthesis, and regulatory mechanism of wheat storage proteins and their impacts on wheat end-product quality.
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Affiliation(s)
- Yanchun Peng
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yun Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Zitong Yu
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jing Dong
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- *Correspondence: Wujun Ma,
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16
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The Gluten-Free Diet for Celiac Disease and Beyond. Nutrients 2021; 13:nu13113993. [PMID: 34836247 PMCID: PMC8625243 DOI: 10.3390/nu13113993] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
The gluten-free diet (GFD) has gained popularity beyond its main medical indication as the treatment for gluten-induced immune-mediated disorders such as celiac disease (CD), dermatitis herpetiformis, gluten ataxia, wheat allergy, and non-celiac gluten sensitivity. However, the diet carries some disadvantages such as elevated costs, nutritional deficiencies, and social and psychological barriers. The present work aims to review indications, proven benefits, and adverse events of a gluten-free diet. Close follow-up with patients following the diet is recommended. More data is needed to assess the effectiveness of the diet in managing mental and cognitive disorders and to establish a connection between the brain and gluten.
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Nye-Wood MG, Juhász A, Bose U, Colgrave ML. Proteome Analysis and Epitope Mapping in a Commercial Reduced-Gluten Wheat Product. Front Nutr 2021; 8:705822. [PMID: 34458308 PMCID: PMC8385123 DOI: 10.3389/fnut.2021.705822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/16/2021] [Indexed: 11/30/2022] Open
Abstract
Gluten related disorders, such as coeliac disease, wheat allergy and baker's asthma are triggered by proteins present in food products made from wheat and related cereal species. The only treatment of these medical illnesses is a strict gluten-free diet; however, gluten-free products that are currently available in the market can have lower nutritional quality and are more expensive than traditional gluten containing cereal products. These constraints have led to the development of gluten-free or gluten-reduced ingredients. In this vein, a non-GMO wheat flour that purports to contain "65% less allergenic gluten" was recently brought to market. The present study aims to understand the alteration of the proteome profile of this wheat flour material. Liquid chromatography-mass spectrometry was used to investigate the proteome profile of the novel wheat flour, which was contrasted to a wheat flour control. Using both trypsin and chymotrypsin digests and a combined database search, 564 unique proteins were identified with 99% confidence. These proteins and the specific peptides used to identify them were mapped to the wheat genome to reveal the associated chromosomal regions in the novel wheat flour and the mixed wheat control. Of note, several ω- and γ-gliadins, and low-molecular weight glutenins mapping to the short arm of chromosome 1, as well as α-gliadins from the chromosome 6 short arm were absent or expressed at lower levels in the novel wheat variety. In contrast, the high-molecular weight glutenins and α-amylase/trypsin inhibitors were notably more abundant in this variety. A targeted quantitation experiment was developed using multiple reaction monitoring assays to quantify 359 tryptic and chymotryptic peptides from gluten and related allergenic proteins revealing a 33% decrease of gluten protein content in the novel wheat flour sample in comparison to mixed wheat control. However, additional mapping of known allergenic epitopes showed the presence of 53% higher allergenic peptides. Overall, the current study highlights the importance of proteomic analyses especially when complemented by sequence analysis and epitope mapping for monitoring immunostimulatory proteins.
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Affiliation(s)
- Mitchell G. Nye-Wood
- School of Science, Edith Cowan University, Perth, WA, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA, Australia
| | - Angéla Juhász
- School of Science, Edith Cowan University, Perth, WA, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA, Australia
| | - Utpal Bose
- School of Science, Edith Cowan University, Perth, WA, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, St Lucia, QLD, Australia
| | - Michelle L. Colgrave
- School of Science, Edith Cowan University, Perth, WA, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Perth, WA, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, St Lucia, QLD, Australia
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Yang Y, Chai Y, Zhang X, Lu S, Zhao Z, Wei D, Chen L, Hu YG. Multi-Locus GWAS of Quality Traits in Bread Wheat: Mining More Candidate Genes and Possible Regulatory Network. FRONTIERS IN PLANT SCIENCE 2020; 11:1091. [PMID: 32849679 PMCID: PMC7411135 DOI: 10.3389/fpls.2020.01091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/02/2020] [Indexed: 05/20/2023]
Abstract
In wheat breeding, improved quality traits, including grain quality and dough rheological properties, have long been a critical goal. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. As a result, 299 quantitative trait nucleotides (QTNs) within 105 regions were identified to be associated with these quality traits in four environments. Of which, 40 core QTN regions were stably detected in at least three environments, 19 of which were novel. Compared with the previous studies, these novel QTN regions explained smaller phenotypic variation, which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits. After characterization of the function and expression in-depth, 67 core candidate genes involved in protein/sugar synthesis, histone modification and the regulation of transcription factor were observed to be associated with the formation of grain quality, which showed that multi-level regulations influenced wheat grain quality. Finally, a preliminary network of gene regulation that may affect wheat quality formation was inferred. This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research, and increased the understanding of wheat quality formation mechanisms. The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in high-quality breeding of bread wheat.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yongmao Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Di Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, China
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Wang D, Li F, Cao S, Zhang K. Genomic and functional genomics analyses of gluten proteins and prospect for simultaneous improvement of end-use and health-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1521-1539. [PMID: 32020238 PMCID: PMC7214497 DOI: 10.1007/s00122-020-03557-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/24/2020] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins, which are important determinants of wheat grain quality traits. The new insights obtained and the availability of precise, versatile and high-throughput genome editing technologies will accelerate simultaneous improvement of wheat end-use and health-related traits. Being a major staple food crop in the world, wheat provides an indispensable source of dietary energy and nutrients to the human population. As worldwide population grows and living standards rise in both developed and developing countries, the demand for wheat with high quality attributes increases globally. However, efficient breeding of high-quality wheat depends on critically the knowledge on gluten proteins, which mainly include several families of prolamin proteins specifically accumulated in the endospermic tissues of grains. Although gluten proteins have been studied for many decades, efficient manipulation of these proteins for simultaneous enhancement of end-use and health-related traits has been difficult because of high complexities in their expression, function and genetic variation. However, recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins. Therefore, the main objective of this review is to summarize the genomic and functional genomics information obtained in the last 10 years on gluten protein chromosome loci and genes and the cis- and trans-factors regulating their expression in the grains, as well as the efforts in elucidating the involvement of gluten proteins in several wheat sensitivities affecting genetically susceptible human individuals. The new insights gathered, plus the availability of precise, versatile and high-throughput genome editing technologies, promise to speed up the concurrent improvement of wheat end-use and health-related traits and the development of high-quality cultivars for different consumption needs.
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Affiliation(s)
- Daowen Wang
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, 15 Longzi Lake College Park, Zhengzhou, 450046, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China.
| | - Feng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China
| | - Shuanghe Cao
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Kunpu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China.
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Juhász A, Colgrave ML, Howitt CA. Developing gluten-free cereals and the role of proteomics in product safety. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.102932] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Diter von Wettstein, Professor of Genetics and Master of Translating Science into Applications. Methods Mol Biol 2020. [PMID: 32277446 DOI: 10.1007/978-1-0716-0356-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The present and subsequent chapters in this volume are dedicated to the life and research of Professor Diter von Wettstein who contributed immensely to the development of science and education. His contributions spanned various fields of science such as genetics, physiology, ultrastructural analysis, molecular biology, genomics, and biotechnology including genome editing. He performed and promoted pioneering research in the fields of epigenetics, directed evolution of enzymes, synthetic biology (promoter and gene optimizations), and genomics (genome sequencing of baker's yeast). Glimpses of his time at the Carlsberg Laboratory and Washington State University, with examples from the research performed at these institutions, are included in this chapter. His life is an inspiration to the next generation of biologists. Despite difficult situations, his persistent efforts and keen desire to learn enabled him to overcome obstacles. He always tried to attain the best, excelling in translating fundamental knowledge into applications.
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Marín-Sanz M, Giménez MJ, Barro F, Savin R. Prolamin Content and Grain Weight in RNAi Silenced Wheat Lines Under Different Conditions of Temperature and Nitrogen Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:314. [PMID: 32265965 PMCID: PMC7100604 DOI: 10.3389/fpls.2020.00314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/03/2020] [Indexed: 05/14/2023]
Abstract
Temperature and nitrogen (N) availability are two important environmental factors that may produce important changes in grain composition during grain filling of bread wheat. In this study, four wheat lines with the down-regulation of gliadins by means of RNA interference (RNAi) have been characterized to determine the effect of thermal stress and N availability on grain weight and quality; with focus on gliadin and glutenin protein fractions. Grain weight was reduced with heat stress (HS) in all RNAi lines, whereas gliadin content was increased in the wild-types. With respect to gliadin content, RNAi lines responded to HS and N availability differently from their respective wild-types, except for ω-gliadin content, indicating a very clear stability of silencing under different environmental conditions. In a context of increased temperature and HS events, and in environments with different N availability, the RNAi lines with down-regulated gliadins seem well suited for the production of wheat grain with low gliadin content.
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Affiliation(s)
- Miriam Marín-Sanz
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, Spain
| | - María J. Giménez
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, Spain
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, Spain
| | - Roxana Savin
- Department of Crop and Forest Sciences, University of Lleida, Lleida, Spain
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Osorio CE, Wen N, Mejías JH, Mitchell S, von Wettstein D, Rustgi S. Directed-Mutagenesis of Flavobacterium meningosepticum Prolyl-Oligopeptidase and a Glutamine-Specific Endopeptidase From Barley. Front Nutr 2020; 7:11. [PMID: 32133368 PMCID: PMC7040222 DOI: 10.3389/fnut.2020.00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/28/2020] [Indexed: 12/12/2022] Open
Abstract
Wheat gluten proteins are the known cause of celiac disease. The repetitive tracts of proline and glutamine residues in these proteins make them exceptionally resilient to digestion in the gastrointestinal tract. These indigested peptides trigger immune reactions in susceptible individuals, which could be either an allergic reaction or celiac disease. Gluten exclusion diet is the only approved remedy for such disorders. Recently, a combination of a glutamine specific endoprotease from barley (EP-B2), and a prolyl endopeptidase from Flavobacterium meningosepticum (Fm-PEP), when expressed in the wheat endosperm, were shown to reasonably detoxify immunogenic gluten peptides under simulated gastrointestinal conditions. However useful, these "glutenases" are limited in application due to their denaturation at high temperatures, which most of the food processes require. Variants of these enzymes from thermophilic organisms exist, but cannot be applied directly due to their optimum activity at temperatures higher than 37°C. Though, these enzymes can serve as a reference to guide the evolution of peptidases of mesophilic origin toward thermostability. Therefore, a sequence guided site-saturation mutagenesis approach was used here to introduce mutations in the genes encoding Fm-PEP and EP-B2. A thermostable variant of Fm-PEP capable of surviving temperatures up to 90°C and EP-B2 variant with a thermostability of up 60°C were identified using this approach. However, the level of thermostability achieved is not sufficient; the present study has provided evidence that the thermostability of glutenases can be improved. And this pilot study has paved the way for more detailed structural studies in the future to obtain variants of Fm-PEP and EP-B2 that can survive temperatures ~100°C to allow their packing in grains and use of such grains in the food industry.
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Affiliation(s)
- Claudia E. Osorio
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- Agriaquaculture Nutritional Genomic Center, Temuco, Chile
| | - Nuan Wen
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Jaime H. Mejías
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco, Chile
| | - Shannon Mitchell
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
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Rustgi S, Kashyap S, Ankrah N, von Wettstein D. Use of Microspore-Derived Calli as Explants for Biolistic Transformation of Common Wheat. Methods Mol Biol 2020; 2124:263-279. [PMID: 32277459 DOI: 10.1007/978-1-0716-0356-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
There are specific advantages of using microspores as explants: (1) A small number of explant donors are required to obtain the desired number of pollen embryoids for genetic transformation and (2) microspores constitute a synchronous mass of haploid cells, which are transformable by various means and convertible to doubled haploids therefore allow production of homozygous genotypes in a single generation. Additionally, it has been demonstrated in wheat and other crops that microspores can be easily induced to produce embryoids and biolistic approach to produce a large number of transformants. In view of these listed advantages, we optimized the use of microspore-derived calli for biolistic transformation of wheat. The procedure takes about 6 months to obtain the viable transformants in the spring wheat background. In the present communication, we demonstrated the use of this method to produce the reduced immunogenicity wheat genotypes.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, USA. .,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
| | - Samneet Kashyap
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Centre, Florence, SC, USA
| | - Nii Ankrah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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Sánchez-León S, Giménez MJ, Comino I, Sousa C, López Casado MÁ, Torres MI, Barro F. Stimulatory Response of Celiac Disease Peripheral Blood Mononuclear Cells Induced by RNAi Wheat Lines Differing in Grain Protein Composition. Nutrients 2019; 11:nu11122933. [PMID: 31816892 PMCID: PMC6950052 DOI: 10.3390/nu11122933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022] Open
Abstract
Wheat gluten proteins are responsible for the bread-making properties of the dough but also for triggering important gastrointestinal disorders. Celiac disease (CD) affects approximately 1% of the population in Western countries. The only treatment available is the strict avoidance of gluten in the diet. Interference RNA (RNAi) is an excellent approach for the down-regulation of genes coding for immunogenic proteins related to celiac disease, providing an alternative for the development of cereals suitable for CD patients. In the present work, we report a comparative study of the stimulatory capacity of seven low-gluten RNAi lines differing in grain gluten and non-gluten protein composition, relevant for CD and other gluten pathologies. Peripheral blood mononuclear cells (PBMCs) of 35 patients with active CD were included in this study to assess the stimulatory response induced by protein extracts from the RNAi lines. Analysis of the proliferative response and interferon-gamma (INF-γ) release of PBMCs demonstrated impaired stimulation in response to all RNAi lines. The lower response was provided by lines with a very low content of α- and γ-gliadins, and low or almost devoid of DQ2.5 and p31-43 α-gliadin epitopes. The non-gluten protein seems not to play a key role in PBMC stimulation.
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Affiliation(s)
- Susana Sánchez-León
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible, 14004 Córdoba, Spain; (S.S.-L.); (M.J.G.)
| | - María José Giménez
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible, 14004 Córdoba, Spain; (S.S.-L.); (M.J.G.)
| | - Isabel Comino
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain; (I.C.); (C.S.)
| | - Carolina Sousa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain; (I.C.); (C.S.)
| | | | - María Isabel Torres
- Departamento de Biología Experimental, Campus Universitario Las Lagunillas, 23071 Jaén, Spain;
| | - Francisco Barro
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible, 14004 Córdoba, Spain; (S.S.-L.); (M.J.G.)
- Correspondence:
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Osorio CE, Mejías JH, Rustgi S. Gluten Detection Methods and Their Critical Role in Assuring Safe Diets for Celiac Patients. Nutrients 2019; 11:E2920. [PMID: 31810336 PMCID: PMC6949940 DOI: 10.3390/nu11122920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022] Open
Abstract
Celiac disease, wheat sensitivity, and allergy represent three different reactions, which may occur in genetically predisposed individuals on the ingestion of wheat and derived products with various manifestations. Improvements in the disease diagnostics and understanding of disease etiology unveiled that these disorders are widespread around the globe affecting about 7% of the population. The only known treatment so far is a life-long gluten-free diet, which is almost impossible to follow because of the contamination of allegedly "gluten-free" products. Accidental contamination of inherently gluten-free products could take place at any level from field to shelf because of the ubiquity of these proteins/grains. Gluten contamination of allegedly "gluten-free" products is a constant threat to celiac patients and a major health concern. Several detection procedures have been proposed to determine the level of contamination in products for celiac patients. The present article aims to review the advantages and disadvantages of different gluten detection methods, with emphasis on the recent technology that allows identification of the immunogenic-gluten peptides without the use of antibodies. The possibility to detect gluten contamination by different approaches with similar or better detection efficiency in different raw and processed foods will guarantee the safety of the foods for celiac patients.
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Affiliation(s)
- Claudia E. Osorio
- Agriaquaculture Nutritional Genomic Center, CGNA, Las Heras 350, Temuco 4781158, Chile
| | - Jaime H. Mejías
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco 4880000, Chile
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA
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Parrilla-Doblas JT, Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. Active DNA Demethylation in Plants. Int J Mol Sci 2019; 20:E4683. [PMID: 31546611 PMCID: PMC6801703 DOI: 10.3390/ijms20194683] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.
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Affiliation(s)
- Jara Teresa Parrilla-Doblas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
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28
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Rustgi S, Shewry P, Brouns F, Deleu LJ, Delcour JA. Wheat Seed Proteins: Factors Influencing Their Content, Composition, and Technological Properties, and Strategies to Reduce Adverse Reactions. Compr Rev Food Sci Food Saf 2019; 18:1751-1769. [PMID: 33336954 DOI: 10.1111/1541-4337.12493] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/16/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Abstract
Wheat is the primary source of nutrition for many, especially those living in developing countries, and wheat proteins are among the most widely consumed dietary proteins in the world. However, concerns about disorders related to the consumption of wheat and/or wheat gluten proteins have increased sharply in the last 20 years. This review focuses on wheat gluten proteins and amylase trypsin inhibitors, which are considered to be responsible for eliciting most of the intestinal and extraintestinal symptoms experienced by susceptible individuals. Although several approaches have been proposed to reduce the exposure to gluten or immunogenic peptides resulting from its digestion, none have proven sufficiently effective for general use in coeliac-safe diets. Potential approaches to manipulate the content, composition, and technological properties of wheat proteins are therefore discussed, as well as the effects of using gluten isolates in various food systems. Finally, some aspects of the use of gluten-free commodities are discussed.
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Affiliation(s)
- Sachin Rustgi
- Dept. of Plant and Environmental Sciences, School of Health Research, Clemson Univ. Pee Dee Research and Education Centre, Florence, SC, U.S.A.,Dept. of Crop and Soil Sciences, Washington State Univ., Pullman, WA, U.S.A
| | - Peter Shewry
- Rothamsted Research, Harpenden, Hertfordshire, U.K
| | - Fred Brouns
- Dept. of Human Biology, School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht Univ., Universiteitssingel 50, 6200, MD, Maastricht, the Netherlands
| | - Lomme J Deleu
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, B-3001, Leuven, Belgium
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Jouanin A, Schaart JG, Boyd LA, Cockram J, Leigh FJ, Bates R, Wallington EJ, Visser RGF, Smulders MJM. Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α- and γ-gliadin gene families. BMC PLANT BIOLOGY 2019; 19:333. [PMID: 31370789 PMCID: PMC6670228 DOI: 10.1186/s12870-019-1889-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/17/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1-2% of the human population. Wheat varieties or accessions containing only safe gluten have not been identified and conventional breeding alone struggles to achieve such a goal, as the epitopes occur in gluten proteins encoded by five multigene families, these genes are partly located in tandem arrays, and bread wheat is allohexaploid. Gluten immunogenicity can be reduced by modification or deletion of epitopes. Mutagenesis technologies, including CRISPR/Cas9, provide a route to obtain bread wheat containing gluten proteins with fewer immunogenic epitopes. RESULTS In this study, we analysed the genetic diversity of over 600 α- and γ-gliadin gene sequences to design six sgRNA sequences on relatively conserved domains that we identified near coeliac disease epitopes. They were combined in four CRISPR/Cas9 constructs to target the α- or γ-gliadins, or both simultaneously, in the hexaploid bread wheat cultivar Fielder. We compared the results with those obtained with random mutagenesis in cultivar Paragon by γ-irradiation. For this, Acid-PAGE was used to identify T1 grains with altered gliadin protein profiles compared to the wild-type endosperm. We first optimised the interpretation of Acid-PAGE gels using Chinese Spring deletion lines. We then analysed the changes generated in 360 Paragon γ-irradiated lines and in 117 Fielder CRISPR/Cas9 lines. Similar gliadin profile alterations, with missing protein bands, could be observed in grains produced by both methods. CONCLUSIONS The results demonstrate the feasibility and efficacy of using CRISPR/Cas9 to simultaneously edit multiple genes in the large α- and γ-gliadin gene families in polyploid bread wheat. Additional methods, generating genomics and proteomics data, will be necessary to determine the exact nature of the mutations generated with both methods.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University and Research, Plant Breeding, Wageningen, The Netherlands
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Jan G. Schaart
- Wageningen University and Research, Plant Breeding, Wageningen, The Netherlands
| | - Lesley A. Boyd
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - James Cockram
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Fiona J. Leigh
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
| | - Ruth Bates
- The John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, UK
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Moehs CP, Austill WJ, Holm A, Large TAG, Loeffler D, Mullenberg J, Schnable PS, Skinner W, van Boxtel J, Wu L, McGuire C. Development of Decreased-Gluten Wheat Enabled by Determination of the Genetic Basis of lys3a Barley. PLANT PHYSIOLOGY 2019; 179:1692-1703. [PMID: 30696748 PMCID: PMC6446766 DOI: 10.1104/pp.18.00771] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/17/2019] [Indexed: 05/08/2023]
Abstract
Celiac disease is the most common food-induced enteropathy in humans, with a prevalence of approximately 1% worldwide. It is induced by digestion-resistant, proline- and glutamine-rich seed storage proteins, collectively referred to as gluten, found in wheat (Triticum aestivum). Related prolamins are present in barley (Hordeum vulgare) and rye (Secale cereale). The incidence of both celiac disease and a related condition called nonceliac gluten sensitivity is increasing. This has prompted efforts to identify methods of lowering gluten in wheat, one of the most important cereal crops. Here, we used bulked segregant RNA sequencing and map-based cloning to identify the genetic lesion underlying a recessive, low-prolamin mutation (lys3a) in diploid barley. We confirmed the mutant identity by complementing the lys3a mutant with a transgenic copy of the wild-type barley gene and then used targeting-induced local lesions in genomes to identify induced single-nucleotide polymorphisms in the three homeologs of the corresponding wheat gene. Combining inactivating mutations in the three subgenomes of hexaploid bread wheat in a single wheat line lowered gliadin and low-molecular-weight glutenin accumulation by 50% to 60% and increased free and protein-bound lysine by 33%.
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Affiliation(s)
| | | | - Aaron Holm
- Arcadia Biosciences, Davis, California 95618
| | | | | | | | - Patrick S Schnable
- Data2Bio, 2079 Roy J. Carver Co-Lab, Ames, Iowa 50011
- 2035B Roy J. Carver Co-Lab, Iowa State University, Ames, Iowa 50011
| | | | | | - Liying Wu
- Arcadia Biosciences, Davis, California 95618
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García-Molina MD, Giménez MJ, Sánchez-León S, Barro F. Gluten Free Wheat: Are We There? Nutrients 2019; 11:E487. [PMID: 30813572 PMCID: PMC6470674 DOI: 10.3390/nu11030487] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022] Open
Abstract
Gluten proteins, major determinants of the bread-making quality of wheat, are related to several digestive disorders. Advances in plant genetic breeding have allowed the production of wheat lines with very low gliadin content through the use of RNAi and gene editing technologies. In this review, we carried out a comprehensive study of the application of these cutting-edge technologies towards the development of wheat lines devoid of immunogenic gluten, and their genetic, nutritional and clinical characterization. One line, named E82, showed outstanding nutritional properties, with very low immunogenic gluten and a low stimulation capacity of T-cells from celiac patients. Moreover, a clinical trial with non-celiac wheat sensitivity (NCWS) patients showed that the consumption of bread made with this E82 low gliadin line induced positive changes in the gut microbiota composition.
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Affiliation(s)
- María Dolores García-Molina
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), 14004 Córdoba, Spain.
- DAFNE Department, University of Tuscia, 01100 Viterbo, Italy.
| | - María José Giménez
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), 14004 Córdoba, Spain.
| | - Susana Sánchez-León
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), 14004 Córdoba, Spain.
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), 14004 Córdoba, Spain.
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32
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Rai S, Kaur A, Chopra CS. Gluten-Free Products for Celiac Susceptible People. Front Nutr 2018; 5:116. [PMID: 30619866 PMCID: PMC6304385 DOI: 10.3389/fnut.2018.00116] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/12/2018] [Indexed: 01/20/2023] Open
Abstract
The gluten protein of wheat triggers an immunological reaction in some gluten-sensitive people with HLA-DQ2/8 genotypes, which leads to Celiac disease (CD) with symptomatic damage in the small intestinal villi. Glutenin and gliadin are two major components of gluten that are essentially required for developing a strong protein network for providing desired viscoelasticity of dough. Many non-gluten cereals and starches (rice, corn, sorghum, millets, and potato/pea starch) and various gluten replacers (xanthan and guar gum) have been used for retaining the physical-sensorial properties of gluten-free, cereal-based products. This paper reviews the recent advances in the formulation of cereal-based, gluten-free products by utilizing alternate flours, starches, gums, hydrocolloids, enzymes, novel ingredients, and processing techniques. The pseudo cereals amaranth, quinoa, and buckwheat, are promising in gluten-free diet formulation. Genetically-modified wheat is another promising area of research, where successful attempts have been made to silence the gliadin gene of wheat using RNAi techniques. The requirement of quantity and quality for gluten-free packaged foods is increasing consistently at a faster rate than lactose-free and diabetic-friendly foods. More research needs to be focused on cereal-based, gluten-free beverages to provide additional options for CD sufferers.
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Affiliation(s)
- Sweta Rai
- Department of Food Science and Technology, G. B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Amarjeet Kaur
- Division of Food Science and Technology, Punjab Agricultural University, Ludhiana, India
| | - C S Chopra
- Department of Food Science and Technology, G. B. Pant University of Agriculture and Technology, Pantnagar, India
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Development of wheat genotypes expressing a glutamine-specific endoprotease from barley and a prolyl endopeptidase from Flavobacterium meningosepticum or Pyrococcus furiosus as a potential remedy to celiac disease. Funct Integr Genomics 2018; 19:123-136. [PMID: 30159724 DOI: 10.1007/s10142-018-0632-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Abstract
Ubiquitous nature of prolamin proteins dubbed gluten from wheat and allied cereals imposes a major challenge in the treatment of celiac disease, an autoimmune disorder with no known treatment other than abstinence diet. Administration of hydrolytic glutenases as food supplement is an alternative to deliver the therapeutic agents directly to the small intestine, where sensitization of immune system and downstream reactions take place. The aim of the present research was to evaluate the capacity of wheat grain to express and store hydrolytic enzymes capable of gluten detoxification. For this purpose, wheat scutellar calli were biolistically transformed to generate plants expressing a combination of glutenase genes for prolamin detoxification. Digestion of prolamins with barley endoprotease B2 (EP-HvB2) combined with Flavobacterium meningosepticum prolyl endopeptidase (PE-FmPep) or Pyrococcus furiosus prolyl endopeptidase (PE-PfuPep) significantly reduced (up to 67%) the amount of the indigestible gluten peptides of all prolamin families tested. Seven of the 168 generated lines showed inheritance of transgene to the T2 generation. Reversed phase high-performance liquid chromatography of gluten extracts under simulated gastrointestinal conditions allowed the identification of five T2 lines that contained significantly reduced amounts of immunogenic, celiac disease-provoking gliadin peptides. These findings were complemented by the R5 ELISA test results where up to 72% reduction was observed in the content of immunogenic peptides. The developed wheat genotypes open new horizons for treating celiac disease by an intraluminal enzyme therapy without compromising their agronomical performance.
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Brew-Appiah RAT, York ZB, Krishnan V, Roalson EH, Sanguinet KA. Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat. PLoS One 2018; 13:e0201439. [PMID: 30074999 PMCID: PMC6075773 DOI: 10.1371/journal.pone.0201439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
A comprehensive understanding of wheat responses to environmental stress will contribute to the long-term goal of feeding the planet. ALERNATIVE OXIDASE (AOX) genes encode proteins involved in a bypass of the electron transport chain and are also known to be involved in stress tolerance in multiple species. Here, we report the identification and characterization of the AOX gene family in diploid and hexaploid wheat. Four genes each were found in the diploid ancestors Triticum urartu, and Aegilops tauschii, and three in Aegilops speltoides. In hexaploid wheat (Triticum aestivum), 20 genes were identified, some with multiple splice variants, corresponding to a total of 24 proteins for those with observed transcription and translation. These proteins were classified as AOX1a, AOX1c, AOX1e or AOX1d via phylogenetic analysis. Proteins lacking most or all signature AOX motifs were assigned to putative regulatory roles. Analysis of protein-targeting sequences suggests mixed localization to the mitochondria and other organelles. In comparison to the most studied AOX from Trypanosoma brucei, there were amino acid substitutions at critical functional domains indicating possible role divergence in wheat or grasses in general. In hexaploid wheat, AOX genes were expressed at specific developmental stages as well as in response to both biotic and abiotic stresses such as fungal pathogens, heat and drought. These AOX expression patterns suggest a highly regulated and diverse transcription and expression system. The insights gained provide a framework for the continued and expanded study of AOX genes in wheat for stress tolerance through breeding new varieties, as well as resistance to AOX-targeted herbicides, all of which can ultimately be used synergistically to improve crop yield.
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Affiliation(s)
- Rhoda A. T. Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Zara B. York
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Vandhana Krishnan
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University, Stanford, United States of America
| | - Eric H. Roalson
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Zhang Y, Li D, Zhang D, Zhao X, Cao X, Dong L, Liu J, Chen K, Zhang H, Gao C, Wang D. Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:857-866. [PMID: 29570880 DOI: 10.1111/tpj.13903] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
GW2 is emerging as a key genetic determinant of grain weight in cereal crops; it has three homoeologs (TaGW2-A1, -B1 and -D1) in hexaploid common wheat (Triticum aestivum L.). Here, by analyzing the gene editing mutants that lack one (B1 or D1), two (B1 and D1) or all three (A1, B1 and D1) homoeologs of TaGW2, several insights are gained into the functions of TaGW2-B1 and -D1 in common wheat grain traits. First, both TaGW2-B1 and -D1 affect thousand-grain weight (TGW) by influencing grain width and length, but the effect conferred by TaGW2-B1 is stronger than that of TaGW2-D1. Second, there exists functional interaction between TaGW2 homoeologs because the TGW increase shown by a double mutant (lacking B1 and D1) was substantially larger than that of their single mutants. Third, both TaGW2-B1 and -D1 modulate cell number and length in the outer pericarp of developing grains, with TaGW2-B1 being more potent. Finally, TaGW2 homoeologs also affect grain protein content as this parameter was generally increased in the mutants, especially in the lines lacking two or three homoeologs. Consistent with this finding, two wheat end-use quality-related parameters, flour protein content and gluten strength, were considerably elevated in the mutants. Collectively, our data shed light on functional difference between and additive interaction of TaGW2 homoeologs in the genetic control of grain weight and protein content traits in common wheat, which may accelerate further research on this important gene and its application in wheat improvement.
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Affiliation(s)
- Yi Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Da Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dingbo Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoge Zhao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuemin Cao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinxing Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kunling Chen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huawei Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Caixia Gao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Zhu J, Fang L, Yu J, Zhao Y, Chen F, Xia G. 5-Azacytidine treatment and TaPBF-D over-expression increases glutenin accumulation within the wheat grain by hypomethylating the Glu-1 promoters. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:735-746. [PMID: 29214328 DOI: 10.1007/s00122-017-3032-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 12/01/2017] [Indexed: 05/12/2023]
Abstract
5-azaC treatment and TaPBF - D over-expression decrease C-methylation status of three Glu - 1 gene promoters, and aid in enhancing the expression of the Glu - 1 genes. The wheat glutenins exert a strong influence over dough elasticity, but the regulation of their encoding genes has not been firmly established. Following treatment with 5-azacytidine (5-azaC), both the weight and glutenin content of the developing and mature grains were significantly increased. The abundance of transcript produced by the Glu-1 genes (encoding high-molecular-weight glutenin subunits), as well as those encoding demethylases and transcriptional factors associated with prolamin synthesis was higher than in grain of non-treated plants. These grains also contained an enhanced content of the prolamin box binding factor (PBF) protein. Bisulfite sequencing indicated that the Glu-1 promoters were less strongly C-methylated in the developing grain than in the flag leaf, while in the developing grain of 5-azaC treated plants, the C-methylation level was lower than in equivalent grains of non-treated plants. Both Glu-1 transcript abundance and glutenin content were higher in the grain set by three independent over-expressors of the D genome homoeolog of TaPBF than in the grain set by wild type plants. When assessed 10 days after flowering, the Glu-1 promoters' methylation level was lower in the developing grains set by the TaPBF-D over-expressor than in the wild type control. An electrophoretic mobility shift assay showed that PBF-D was able to bind in vitro to the P-box of Glu-1By8 and -1Dx2, while a ChIP-qPCR analysis revealed that a lower level of C-methylation in the Glu-1By8 and -1Dx2 promoters improved the TaPBF binding. We suggest that promoter DNA C-methylation is a key determinant of Glu-1 transcription.
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Affiliation(s)
- Jiantang Zhu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Linlin Fang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Jiaqi Yu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Ying Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
| | - Fanguo Chen
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan, 250100, China
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Li Y, Kumar S, Qian W. Active DNA demethylation: mechanism and role in plant development. PLANT CELL REPORTS 2018; 37:77-85. [PMID: 29026973 PMCID: PMC5758694 DOI: 10.1007/s00299-017-2215-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/05/2017] [Indexed: 05/18/2023]
Abstract
Active DNA demethylation (enzymatic removal of methylated cytosine) regulates many plant developmental processes. In Arabidopsis, active DNA demethylation entails the base excision repair pathway initiated by the Repressor of silencing 1/Demeter family of bifunctional DNA glycosylases. In this review, we first present an introduction to the recent advances in our understanding about the mechanisms of active DNA demethylation. We then focus on the role of active DNA demethylation in diverse developmental processes in various plant species, including the regulation of seed development, pollen tube formation, stomatal development, fruit ripening, and nodule development. Finally, we discuss future directions of research in the area of active DNA demethylation.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.
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Wang M, Wang S, Liang Z, Shi W, Gao C, Xia G. From Genetic Stock to Genome Editing: Gene Exploitation in Wheat. Trends Biotechnol 2017; 36:160-172. [PMID: 29102241 DOI: 10.1016/j.tibtech.2017.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
Bread wheat (Triticum aestivum) ranks as one of our most important staple crops. However, its hexaploid nature has complicated our understanding of the genetic bases underlying many of its traits. Historically, functional genetic studies in wheat have focused on identifying natural variations and have contributed to assembling and enriching its genetic stock. Recently, mold-breaking advances in whole genome sequencing, exome-capture based mutant libraries, and genome editing have revolutionized strategies for genetic research in wheat. We review new trends in wheat functional genetic studies along with germplasm conservation and innovation, including the relevance of genetic stocks, and the application of sequencing-based mutagenesis and genome editing. We also highlight the potential of multiplex genome editing toolkits in addressing species-specific challenges in wheat.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China; State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; These authors contributed equally to this work
| | - Shubin Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China; These authors contributed equally to this work
| | - Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China.
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Jouanin A, Gilissen LJWJ, Boyd LA, Cockram J, Leigh FJ, Wallington EJ, van den Broeck HC, van der Meer IM, Schaart JG, Visser RGF, Smulders MJM. Food processing and breeding strategies for coeliac-safe and healthy wheat products. Food Res Int 2017; 110:11-21. [PMID: 30029701 DOI: 10.1016/j.foodres.2017.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 01/01/2023]
Abstract
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University & Research, Wageningen, The Netherlands; NIAB, Cambridge CB3 0LE, UK
| | | | | | | | | | | | | | | | - Jan G Schaart
- Wageningen University & Research, Wageningen, The Netherlands
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Colgrave ML, Byrne K, Blundell M, Heidelberger S, Lane CS, Tanner GJ, Howitt CA. Comparing Multiple Reaction Monitoring and Sequential Window Acquisition of All Theoretical Mass Spectra for the Relative Quantification of Barley Gluten in Selectively Bred Barley Lines. Anal Chem 2016; 88:9127-35. [PMID: 27533879 DOI: 10.1021/acs.analchem.6b02108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Celiac disease (CD) is a disease of the small intestine that occurs in genetically susceptible subjects triggered by the ingestion of cereal gluten proteins for which the only treatment is strict adherence to a life-long gluten-free diet. Barley contains four gluten protein families, and the existence of barley genotypes that do not accumulate the B-, C-, and D-hordeins paved the way for the development of an ultralow gluten phenotype. Using conventional breeding strategies, three null mutations behaving as recessive alleles were combined to create a hordein triple-null barley variety. Proteomics has become an invaluable tool for characterization and quantification of the protein complement of cereal grains. In this study multiple reaction monitoring (MRM) mass spectrometry, viewed as the gold standard for peptide quantification, was compared to the data-independent acquisition strategy known as SWATH-MS (sequential window acquisition of all theoretical mass spectra). SWATH-MS was comparable (p < 0.001) to MRM-MS for 32/33 peptides assessed across the four families of hordeins (gluten) in eight barley lines. The results of SWATH-MS analysis further confirmed the absence of the B-, C-, and D-hordeins in the triple-null barley line and showed significantly reduced levels ranging from <1% to 16% relative to wild-type (WT) cv Sloop for the minor γ-hordein class. SWATH-MS represents a valuable tool for quantitative proteomics based on its ability to generate reproducible data comparable with MRM-MS, but has the added benefits of allowing reinterrogation of data to improve analytical performance, ask new questions, and in this case perform quantification of trypsin-resistant proteins (C-hordeins) through analysis of their semi- or nontryptic fragments.
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Affiliation(s)
| | - Keren Byrne
- CSIRO Agriculture, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Malcolm Blundell
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | | | - Catherine S Lane
- SCIEX, Phoenix House, Lakeside Drive, Centre Park, Warrington, WA1 1RX, U.K
| | - Gregory J Tanner
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Crispin A Howitt
- CSIRO Agriculture, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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Sutton KH, Simmons LD, Cummack JB, Roberts SJ. Production of Flours with Reduced Epitope Content Using Milling Technology. Cereal Chem 2016. [DOI: 10.1094/cchem-10-15-0208-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kevin H. Sutton
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch Mail Centre, Christchurch 8140, New Zealand
| | - Lyall D. Simmons
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch Mail Centre, Christchurch 8140, New Zealand
| | - Jill B. Cummack
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch Mail Centre, Christchurch 8140, New Zealand
| | - Sarah J. Roberts
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch Mail Centre, Christchurch 8140, New Zealand
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Supplementation of Reduced Gluten Barley Diet with Oral Prolyl Endopeptidase Effectively Abrogates Enteropathy-Associated Changes in Gluten-Sensitive Macaques. Nutrients 2016; 8:nu8070401. [PMID: 27367722 PMCID: PMC4963877 DOI: 10.3390/nu8070401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 02/07/2023] Open
Abstract
Celiac disease (CD) is an autoimmune disorder that affects approximately three million people in the United States. Furthermore, non-celiac gluten sensitivity (NCGS) affects an estimated additional 6% of the population, e.g., 20 million in the U.S. The only effective treatment of CD and NCGS requires complete removal of gluten sources from the diet. While required adherence to a gluten-free diet (GFD) is extremely difficult to accomplish, efforts to develop additional supportive treatments are needed. To facilitate these efforts, we developed a gluten-sensitive (GS) rhesus macaque model to study the effects of novel therapies. Recently reported results from phase one of this project suggest that partial improvement—but not remission—of gluten-induced disease can be accomplished by 100-fold reduction of dietary gluten, i.e., 200 ppm—by replacement of conventional dietary sources of gluten with a mutant, reduced gluten (RG) barley (lys3a)-derived source. The main focus of this (phase two) study was to determine if the inflammatory effects of the residual gluten in lys3a mutant barley grain could be further reduced by oral supplementation with a prolylendopeptidase (PE). Results reveal that PE supplementation of RG barley diet induces more complete immunological, histopathological and clinical remission than RG barley diet alone. The combined effects of RG barley diet and PE supplementation resulted in a further decrease of inflammatory mediators IFN-γ and TNF secretion by peripheral lymphocytes, as well as decreased plasma anti-gliadin and anti-intestinal tissue transglutaminase (TG2) antibodies, diminished active caspase production in small intestinal mucosa, and eliminated clinical diarrhea—all comparable with a gluten-free diet induced remission. In summary, the beneficial results of a combined RG barley and PE administration in GS macaques may warrant the investigation of similar synergistic approaches.
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43
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Technological and Engineering Trends for Production of Gluten-Free Beers. FOOD ENGINEERING REVIEWS 2016. [DOI: 10.1007/s12393-016-9142-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Tanner GJ, Blundell MJ, Colgrave ML, Howitt CA. Creation of the first ultra-low gluten barley (Hordeum vulgare L.) for coeliac and gluten-intolerant populations. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1139-50. [PMID: 26427614 PMCID: PMC5054857 DOI: 10.1111/pbi.12482] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 09/02/2015] [Indexed: 05/08/2023]
Abstract
Coeliac disease is a well-defined condition that is estimated to affect approximately 1% of the population worldwide. Noncoeliac gluten sensitivity is a condition that is less well defined, but is estimated to affect up to 10% of the population, and is often self-diagnosed. At present, the only remedy for both conditions is a lifelong gluten-free diet. A gluten-free diet is often expensive, high in fat and low in fibre, which in themselves can lead to adverse health outcomes. Thus, there is an opportunity to use novel plant breeding strategies to develop alternative gluten-free grains. In this work, we describe the breeding and characterization of a novel ultra-low gluten (ULG) barley variety in which the hordein (gluten) content was reduced to below 5 ppm. This was achieved using traditional breeding strategies to combine three recessive alleles, which act independently of each other to lower the hordein content in the parental varieties. The grain of the initial variety was shrunken compared to wild-type barleys. We implemented a breeding strategy to improve the grain size to near wild-type levels and demonstrated that the grains can be malted and brewed successfully. The ULG barley has the potential to provide novel healthy foods and beverages for those who require a gluten-free diet.
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45
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Abstract
Coeliac disease is an intolerance triggered by the ingestion of wheat gluten proteins. It is of increasing concern to consumers and health professionals as its incidence appears to be increasing. The amino acid sequences in gluten proteins that are responsible for triggering responses in sensitive individuals have been identified showing that they vary in distribution among and between different groups of gluten proteins. Conventional breeding may therefore be used to select for gluten protein fractions with lower contents of coeliac epitopes. Molecular breeding approaches can also be used to specifically down-regulate coeliac-toxic proteins or mutate coeliac epitopes within individual proteins. A combination of these approaches may therefore be used to develop a “coeliac-safe” wheat. However, this remains a formidable challenge due to the complex multigenic control of gluten protein composition. Furthermore, any modified wheats must retain acceptable properties for making bread and other processed foods. Not surprisingly, such coeliac-safe wheats have not yet been developed despite over a decade of research. Coeliac disease is of increasing concern as its incidence appears to be increasing. Over 30 amino acid sequences (coeliac epitopes) have been defined. Coeliac epitopes differ in their distribution between wheat gluten proteins. Transgenesis can be used to reduce coeliac-toxic proteins and coeliac epitopes. This can be exploited to develop “coeliac-safe” wheats.
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Affiliation(s)
- Peter R Shewry
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; University of Reading, Whiteknights, Reading, Berkshire RG6 6AH, UK
| | - Arthur S Tatham
- Cardiff School of Heath Sciences, Cardiff Metropolitan University, Llandaff Campus, Western Avenue, Cardiff CF5 2YB, UK
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Guo W, Yang H, Liu Y, Gao Y, Ni Z, Peng H, Xin M, Hu Z, Sun Q, Yao Y. The wheat transcription factor TaGAMyb recruits histone acetyltransferase and activates the expression of a high-molecular-weight glutenin subunit gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:347-59. [PMID: 26332346 DOI: 10.1111/tpj.13003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 05/23/2023]
Abstract
Glutenin proteins in wheat (Triticum aestivum L.) flour confer unique viscoelastic properties to dough products and, therefore, the concentration and composition of the glutenin proteins determine its end-use value. However, the mechanisms governing the glutenin gene expression remain elusive. In this study, we report that wheat TaGAMyb activates the high-molecular-weight glutenin subunit genes (TaGLU) through recruiting the histone acetyltransferase GCN5. By sequencing the promoters of TaGLU-1 genes from 40 modern wheat cultivars, we identified eight types of TaGAMyb binding motifs and verified these by electrophoretic mobility shift assays. The number of TaGAMyb binding motifs in TaGLU-1 genes is correlated with the abundance of glutenin in different cultivars. Chromatin immunoprecipitation plus polymerase chain reaction (ChIP-PCR) analysis reveals that TaGCN5 directly targets the promoters of TaGLU-1 genes in wheat endosperm. We find that TaGAMyb physically interacts with the wheat histone acetyltransferase TaGCN5 and also interacts with Arabidopsis thaliana AtGCN5. TaGAMyb ectopically expressed in Arabidopsis binds to the TaGLU-1Dy promoter on a TaGLU-1Dy transgene and activates its expression. AtGCN5 also targets the TaGLU-1Dy transgene and is involved in the establishment of acetylation at H3K9 and H3K14. These results demonstrate that TaGAMyb plays a dual role in activating expression of glutenin gene by directly binding to the TaGLU promoter and by recruiting GCN5 to modulate histone acetylation during wheat endosperm development.
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Affiliation(s)
- Weiwei Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Hua Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongqiang Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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47
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Qin P, Wang L, Liu K, Mao S, Li Z, Gao S, Shi H, Liu Y. Genomewide association study of Aegilops tauschii traits under seedling-stage cadmium stress. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.cj.2015.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Wang M, Wang S, Xia G. From genome to gene: a new epoch for wheat research? TRENDS IN PLANT SCIENCE 2015; 20:380-387. [PMID: 25887708 DOI: 10.1016/j.tplants.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Genetic research for bread wheat (Triticum aestivum), a staple crop around the world, has been impeded by its complex large hexaploid genome that contains a high proportion of repetitive DNA. Recent advances in sequencing technology have now overcome these challenges and led to genome drafts for bread wheat and its progenitors as well as high-resolution transcriptomes. However, the exploitation of these data for identifying agronomically important genes in wheat is lagging behind. We review recent wheat genome sequencing achievements and focus on four aspects of strategies and future hotspots for wheat improvement: positional cloning, 'omics approaches, combining forward and reverse genetics, and epigenetics.
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Affiliation(s)
- Meng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Shubin Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China.
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49
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Makai S, Éva C, Tamás L, Juhász A. Multiple elements controlling the expression of wheat high molecular weight glutenin paralogs. Funct Integr Genomics 2015; 15:661-72. [PMID: 25893709 DOI: 10.1007/s10142-015-0441-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/24/2015] [Accepted: 04/06/2015] [Indexed: 01/23/2023]
Abstract
Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments coupled with cis-regulatory elements enrichment study and cluster analysis can be used to define modular gene programs and regulatory networks. Unfortunately, the high molecular weight glutenin subunits of wheat (Triticum aestivum) are more similar than microarray data alone would allow to distinguish between the three homoeologous gene pairs. However, combining complementary DNA (cDNA) expression libraries with microarray data, a co-expressional network was built that highlighted the hidden differences between these highly similar genes. Duplex clusters of cis-regulatory elements were used to focus the co-expressional network of transcription factors to the putative regulatory network of Glu-1 genes. The focused network helped to identify several transcriptional gene programs in the endosperm. Many of these programs demonstrated a conserved temporal pattern across the studied genotypes; however, few others showed variance. Based on this network, transient gene expression assays were performed with mutated promoters to inspect the control of tissue specificity. Results indicated that the interactions of the ABRE│CBF cluster with distal promoter regions may have a dual role in regulation by both recruiting the transcription complex as well as suppressing it in non-endosperm tissue. A putative model of regulation is discussed.
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Affiliation(s)
- Szabolcs Makai
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary.,Department of Plant Physiology and Molecular Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Csaba Éva
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary
| | - László Tamás
- Department of Plant Physiology and Molecular Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Angéla Juhász
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary.
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The effects of reduced gluten barley diet on humoral and cell-mediated systemic immune responses of gluten-sensitive rhesus macaques. Nutrients 2015; 7:1657-71. [PMID: 25756783 PMCID: PMC4377872 DOI: 10.3390/nu7031657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/11/2015] [Accepted: 02/27/2015] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CD) affects approximately 1% of the general population while an estimated additional 6% suffers from a recently characterized, rapidly emerging, similar disease, referred to as non-celiac gluten sensitivity (NCGS). The only effective treatment of CD and NCGS requires removal of gluten sources from the diet. Since required adherence to a gluten-free diet (GFD) is difficult to accomplish, efforts to develop alternative treatments have been intensifying in recent years. In this study, the non-human primate model of CD/NCGS, e.g., gluten-sensitive rhesus macaque, was utilized with the objective to evaluate the treatment potential of reduced gluten cereals using a reduced gluten (RG; 1% of normal gluten) barley mutant as a model. Conventional and RG barleys were used for the formulation of experimental chows and fed to gluten-sensitive (GS) and control macaques to determine if RG barley causes a remission of dietary gluten-induced clinical and immune responses in GS macaques. The impacts of the RG barley diet were compared with the impacts of the conventional barley-containing chow and the GFD. Although remission of the anti-gliadin antibody (AGA) serum responses and an improvement of clinical diarrhea were noted after switching the conventional to the RG barley diet, production of inflammatory cytokines, e.g., interferon-gamma (IFN-γ), tumor necrosis factor (TNF) and interleukin-8 (IL-8) by peripheral CD4+ T helper lymphocytes, persisted during the RG chow treatment and were partially abolished only upon re-administration of the GFD. It was concluded that the RG barley diet might be used for the partial improvement of gluten-induced disease but its therapeutic value still requires upgrading—by co-administration of additional treatments.
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