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Koch A, Kogel KH. New wind in the sails: improving the agronomic value of crop plants through RNAi-mediated gene silencing. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:821-31. [PMID: 25040343 DOI: 10.1111/pbi.12226] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/06/2014] [Accepted: 05/27/2014] [Indexed: 05/21/2023]
Abstract
RNA interference (RNAi) has emerged as a powerful genetic tool for scientific research over the past several years. It has been utilized not only in fundamental research for the assessment of gene function, but also in various fields of applied research, such as human and veterinary medicine and agriculture. In plants, RNAi strategies have the potential to allow manipulation of various aspects of food quality and nutritional content. In addition, the demonstration that agricultural pests, such as insects and nematodes, can be killed by exogenously supplied RNAi targeting their essential genes has raised the possibility that plant predation can be controlled by lethal RNAi signals generated in planta. Indeed, recent evidence argues that this strategy, called host-induced gene silencing (HIGS), is effective against sucking insects and nematodes; it also has been shown to compromise the growth and development of pathogenic fungi, as well as bacteria and viruses, on their plant hosts. Here, we review recent studies that reveal the enormous potential RNAi strategies hold not only for improving the nutritive value and safety of the food supply, but also for providing an environmentally friendly mechanism for plant protection.
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Affiliation(s)
- Aline Koch
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology and Applied Zoology, Justus Liebig University, Giessen, Germany
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Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci U S A 2014; 111:10642-7. [PMID: 25002488 DOI: 10.1073/pnas.1410761111] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cytosine methylation at CG sites ((m)CG) plays critical roles in development, epigenetic inheritance, and genome stability in mammals and plants. In the dicot model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal CG methylase, functions to maintain (m)CG during DNA replication, with its null mutation resulting in global hypomethylation and pleiotropic developmental defects. Null mutation of a critical CG methylase has not been characterized at a whole-genome level in other higher eukaryotes, leaving the generality of the Arabidopsis findings largely speculative. Rice is a model plant of monocots, to which many of our important crops belong. Here we have characterized a null mutant of OsMet1-2, the major CG methylase in rice. We found that seeds homozygous for OsMet1-2 gene mutation (OsMET1-2(-/-)), which directly segregated from normal heterozygote plants (OsMET1-2(+/-)), were seriously maldeveloped, and all germinated seedlings underwent swift necrotic death. Compared with wild type, genome-wide loss of (m)CG occurred in the mutant methylome, which was accompanied by a plethora of quantitative molecular phenotypes including dysregulated expression of diverse protein-coding genes, activation and repression of transposable elements, and altered small RNA profiles. Our results have revealed conservation but also distinct functional differences in CG methylases between rice and Arabidopsis.
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53
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Gilissen LJ, van der Meer IM, Smulders MJ. Reducing the incidence of allergy and intolerance to cereals. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2014.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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54
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Rosell CM, Barro F, Sousa C, Mena MC. Cereals for developing gluten-free products and analytical tools for gluten detection. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2013.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Analysis of wheat prolamins, the causative agents of celiac sprue, using reversed phase high performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). Nutrients 2014; 6:1578-97. [PMID: 24739977 PMCID: PMC4011052 DOI: 10.3390/nu6041578] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 12/20/2022] Open
Abstract
Wheat prolamins, commonly known as "gluten", are a complex mixture of 71-78 proteins, which constitute ~80% of the proteins in the wheat grains and supply 50% of the global dietary protein demand. Prolamins are also responsible for numerous gluten-induced disorders and determine the unique visco-elastic properties of the wheat dough. These properties necessitate the reliable determination of the prolamin composition in wheat grains and their derived products. Therefore, this study examined the impact of HPLC conditions, including column type, column temperature, flow rate, and the gradient of polar and non-polar solvents in the mobile phase, to improve the analytical resolution of prolamins. The following conditions were found optimal for analyses: column temperature 60 °C, flow rate 1.0 mL/min and an elution gradient of 20%-60% of 0.1% trifluoroacetic acid + acetonitrile in 60 min. For further improvement of resolution, gliadin and glutenin extracts were analyzed using MALDI-TOF-MS in combination with HPLC fractionation. Two semi-quantitative methods, densitometry of stained polyacrylamide gels and HPLC, were used to determine relative prolamin quantities and the correspondence between the methods was established. The combinatorial gluten analyses approach developed during the present study was used to analyze prolamin profiles of wheat transformants expressing DEMETER silencing artificial microRNA, and the results are discussed.
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Brooks SC, Fischer RL, Huh JH, Eichman BF. 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. Biochemistry 2014; 53:2525-32. [PMID: 24678721 PMCID: PMC4004242 DOI: 10.1021/bi5002294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Methylation of cytosine to 5-methylcytosine
(5mC) is important
for gene expression, gene imprinting, X-chromosome inactivation, and
transposon silencing. Active demethylation in animals is believed
to proceed by DNA glycosylase removal of deaminated or oxidized 5mC.
In plants, 5mC is removed from the genome directly by the DEMETER
(DME) family of DNA glycosylases. Arabidopsis thaliana DME excises 5mC to activate expression of maternally imprinted genes.
Although the related Repressor of Silencing 1 (ROS1) enzyme has been
characterized, the molecular basis for 5mC recognition by DME has
not been investigated. Here, we present a structure–function
analysis of DME and the related DME-like 3 (DML3) glycosylases for
5mC and its oxidized derivatives. Relative to 5mC, DME and DML3 exhibited
robust activity toward 5-hydroxymethylcytosine, limited activity for
5-carboxylcytosine, and no activity for 5-formylcytosine. We used
homology modeling and mutational analysis of base excision and DNA
binding to identify residues important for recognition of 5mC within
the context of DNA and inside the enzyme active site. Our results
indicate that the 5mC binding pocket is composed of residues from
discrete domains and is responsible for discrimination against 5mC
derivatives, and suggest that DME, ROS1, and DML3 utilize subtly different
mechanisms to probe the DNA duplex for cytosine modifications.
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Affiliation(s)
- Sonja C Brooks
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
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Gil-Humanes J, Pistón F, Altamirano-Fortoul R, Real A, Comino I, Sousa C, Rosell CM, Barro F. Reduced-gliadin wheat bread: an alternative to the gluten-free diet for consumers suffering gluten-related pathologies. PLoS One 2014; 9:e90898. [PMID: 24621595 PMCID: PMC3951262 DOI: 10.1371/journal.pone.0090898] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 02/06/2014] [Indexed: 12/20/2022] Open
Abstract
Wheat flour cannot be tolerated by those who suffer allergies to gluten. Human pathologies associated with grain proteins have increased worldwide in recent years, and the only effective treatment available is a lifelong gluten-free diet, which is complicated to follow and detrimental to gut health. This manuscript describes the development of wheat bread potentially suitable for celiac patients and other gluten-intolerant individuals. We have made bread using wheat flour with very low content of the specific gluten proteins (near gliadin-free) that are the causal agents for pathologies such as celiac disease. Loaves were compared with normal wheat breads and rice bread. Organoleptic, nutritional, and immunotoxic properties were studied. The reduced-gliadin breads showed baking and sensory properties, and overall acceptance, similar to those of normal flour, but with up to 97% lower gliadin content. Moreover, the low-gliadin flour has improved nutritional properties since its lysine content is significantly higher than that of normal flour. Conservative estimates indicate that celiac patients could safely consume 67 grams of bread per day that is made with low-gliadin flour. However, additional studies, such as feeding trials with gluten-intolerant patients, are still needed in order to determine whether or not the product can be consumed by the general celiac population, as well as the actual tolerated amount that can be safely ingested. The results presented here offer a major opportunity to improve the quality of life for millions of sufferers of gluten intolerance throughout the world.
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Affiliation(s)
- Javier Gil-Humanes
- Instituto de Agricultura Sostenible, CSIC, Córdoba, Spain
- * E-mail: (JG-H); (FB)
| | | | | | - Ana Real
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Isabel Comino
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Carolina Sousa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Cristina M. Rosell
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain
| | - Francisco Barro
- Instituto de Agricultura Sostenible, CSIC, Córdoba, Spain
- * E-mail: (JG-H); (FB)
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The tip of the "celiac iceberg" in China: a systematic review and meta-analysis. PLoS One 2013; 8:e81151. [PMID: 24324669 PMCID: PMC3852028 DOI: 10.1371/journal.pone.0081151] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/18/2013] [Indexed: 12/29/2022] Open
Abstract
Objective Until recently, celiac disease was considered to be rare in China. We aimed to estimate its true status. Methods By searching the MEDLINE database and four Chinese full-text databases (CNKI, CBM, VIP and WANFANG) (up to August 2012), as well as two HLA allele frequency net databases and the Chinese Statistics Yearbook databases, we systematically reviewed the literature on definite and suspected cases of celiac disease, the predisposing HLA allele frequencies, and on gluten exposure in China. Meta-analysis was performed by analyzing DQ2, DQ8 and DQB1*0201 gene frequencies and heterogeneity in populations from different geographic regions and ethnicities in China. Results At present, the number of reported celiac disease cases is extremely low in China. The frequencies of the HLA-DQ2.5 and HLA-DQ8 haplotypes were 3.4% (95% confidence interval 1.3–5.5%) and 2.1% (0.1–4.1%), respectively. HLA-DQ2 and HLA-DQ8 antigen frequencies were 18.4% (15.0–21.7%) and 8.0% (4.5–11.4%), respectively. The frequency of the DQB1*0201 allele was 10.5% (9.3–11.6%) and it was more common in the northern Chinese than in the southern Chinese populations. The chance of being exposed to gluten is rapidly increasing all over China nowadays. Conclusion The data on HLA haplotyping, in conjunction with increasing wheat consumption, strongly suggests that the occurrence of celiac disease is more common in China than currently reported. Coordinated measures by the Chinese government, medical and agricultural research institutions, and food industries, would be justified to create more awareness about celiac disease and to prevent it becoming a medical and societal burden.
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Kapazoglou A, Drosou V, Argiriou A, Tsaftaris AS. The study of a barley epigenetic regulator, HvDME, in seed development and under drought. BMC PLANT BIOLOGY 2013; 13:172. [PMID: 24175960 PMCID: PMC4228467 DOI: 10.1186/1471-2229-13-172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/17/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Epigenetic factors such as DNA methylation and histone modifications regulate a wide range of processes in plant development. Cytosine methylation and demethylation exist in a dynamic balance and have been associated with gene silencing or activation, respectively. In Arabidopsis, cytosine demethylation is achieved by specific DNA glycosylases, including AtDME (DEMETER) and AtROS1 (REPRESSOR OF SILENCING1), which have been shown to play important roles in seed development. Nevertheless, studies on monocot DNA glycosylases are limited. Here we present the study of a DME homologue from barley (HvDME), an agronomically important cereal crop, during seed development and in response to conditions of drought. RESULTS An HvDME gene, identified in GenBank, was found to encode a protein with all the characteristic modules of DME-family DNA glycosylase proteins. Phylogenetic analysis revealed a high degree of homology to other monocot DME glycosylases, and sequence divergence from the ROS1, DML2 and DML3 orthologues. The HvDME gene contains the 5' and 3' Long Terminal Repeats (LTR) of a Copia retrotransposon element within the 3' downstream region. HvDME transcripts were shown to be present both in vegetative and reproductive tissues and accumulated differentially in different seed developmental stages and in two different cultivars with varying seed size. Additionally, remarkable induction of HvDME was evidenced in response to drought treatment in a drought-tolerant barley cultivar. Moreover, variable degrees of DNA methylation in specific regions of the HvDME promoter and gene body were detected in two different cultivars. CONCLUSION A gene encoding a DNA glycosylase closely related to cereal DME glycosylases was characterized in barley. Expression analysis during seed development and under dehydration conditions suggested a role for HvDME in endosperm development, seed maturation, and in response to drought. Furthermore, differential DNA methylation patterns within the gene in two different cultivars suggested epigenetic regulation of HvDME. The study of a barley DME gene will contribute to our understanding of epigenetic mechanisms operating during seed development and stress response in agronomically important cereal crops.
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Affiliation(s)
- Aliki Kapazoglou
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki GR-57001, Greece
| | - Vicky Drosou
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki GR-57001, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki GR-57001, Greece
| | - Athanasios S Tsaftaris
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki GR-57001, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
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The gluten-free diet: testing alternative cereals tolerated by celiac patients. Nutrients 2013; 5:4250-68. [PMID: 24152755 PMCID: PMC3820072 DOI: 10.3390/nu5104250] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/07/2013] [Accepted: 10/15/2013] [Indexed: 02/07/2023] Open
Abstract
A strict gluten-free diet (GFD) is the only currently available therapeutic treatment for patients with celiac disease, an autoimmune disorder of the small intestine associated with a permanent intolerance to gluten proteins. The complete elimination of gluten proteins contained in cereals from the diet is the key to celiac disease management. However, this generates numerous social and economic repercussions due to the ubiquity of gluten in foods. The research presented in this review focuses on the current status of alternative cereals and pseudocereals and their derivatives obtained by natural selection, breeding programs and transgenic or enzymatic technology, potential tolerated by celiac people. Finally, we describe several strategies for detoxification of dietary gluten. These included enzymatic cleavage of gliadin fragment by Prolyl endopeptidases (PEPs) from different organisms, degradation of toxic peptides by germinating cereal enzymes and transamidation of cereal flours. This information can be used to search for and develop cereals with the baking and nutritional qualities of toxic cereals, but which do not exacerbate this condition.
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Baranska A, Tigchelaar E, Smolinska A, Dallinga JW, Moonen EJC, Dekens JAM, Wijmenga C, Zhernakova A, van Schooten FJ. Profile of volatile organic compounds in exhaled breath changes as a result of gluten-free diet. J Breath Res 2013; 7:037104. [DOI: 10.1088/1752-7155/7/3/037104] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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