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Rybnikov SR, Hübner S, Korol AB. A Numerical Model Supports the Evolutionary Advantage of Recombination Plasticity in Shifting Environments. Am Nat 2024; 203:E78-E91. [PMID: 38358806 DOI: 10.1086/728405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractNumerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario-when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and, optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may also appear beneficial when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared with the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms, such as chromatin epigenetics remodeling.
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2
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Bhushan S, Singh AK, Thakur Y, Baskar R. Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis. BMC PLANT BIOLOGY 2023; 23:152. [PMID: 36944916 PMCID: PMC10031922 DOI: 10.1186/s12870-023-04150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
In the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BSR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation (e.g. BSR (F1 38 = 0.9, F2 38 = 1.14, F3 38 = 1.02, F4 38 = 0.5, F5 38 = 0.76)). On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates (BSR (F1 38 = 0.9, F1 43 = 0.53, F1 48 = 0.79, F1 53 = 0.83 and F2 38 = 1.14, F2 43 = 0.57, F2 48 = 0.64, F2 53 = 0.94). We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.
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Affiliation(s)
- Shashi Bhushan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
| | - Yogendra Thakur
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Ramamurthy Baskar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India.
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3
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Ling Q, Liao J, Liu X, Zhou Y, Qian Y. Genome-Wide Identification of Maize Protein Arginine Methyltransferase Genes and Functional Analysis of ZmPRMT1 Reveal Essential Roles in Arabidopsis Flowering Regulation and Abiotic Stress Tolerance. Int J Mol Sci 2022; 23:12793. [PMID: 36361583 PMCID: PMC9655960 DOI: 10.3390/ijms232112793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 10/29/2023] Open
Abstract
Histone methylation, as one of the important epigenetic regulatory mechanisms, plays a significant role in growth and developmental processes and stress responses of plants, via altering the methylation status or ratio of arginine and lysine residues of histone tails, which can affect the regulation of gene expression. Protein arginine methyltransferases (PRMTs) have been revealed to be responsible for histone methylation of specific arginine residues in plants, which is important for maintaining pleiotropic development and adaptation to abiotic stresses in plants. Here, for the first time, a total of eight PRMT genes in maize have been identified and characterized in this study, named as ZmPRMT1-8. According to comparative analyses of phylogenetic relationship and structural characteristics among PRMT gene family members from several representative species, all maize 8 PRMT proteins were categorized into three distinct subfamilies. Further, schematic structure and chromosome location analyses displayed evolutionarily conserved structure features and an unevenly distribution on maize chromosomes of ZmPRMT genes, respectively. The expression patterns of ZmPRMT genes in different tissues and under various abiotic stresses (heat, drought, and salt) were determined. The expression patterns of ZmPRMT genes indicated that they play a role in regulating growth and development and responses to abiotic stress. Eventually, to verify the biological roles of ZmPRMT genes, the transgenic Arabidopsis plants overexpressing ZmPRMT1 gene was constructed as a typical representative. The results demonstrated that overexpression of ZmPRMT1 can promote earlier flowering time and confer enhanced heat tolerance in transgenic Arabidopsis. Taken together, our results are the first to report the roles of ZmPRMT1 gene in regulating flowering time and resisting heat stress response in plants and will provide a vital theoretical basis for further unraveling the functional roles and epigenetic regulatory mechanism of ZmPRMT genes in maize growth, development and responses to abiotic stresses.
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Affiliation(s)
| | | | | | | | - Yexiong Qian
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Important Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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4
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Thakur RK, Prasad P, Bhardwaj SC, Gangwar OP, Kumar S. Epigenetics of wheat-rust interaction: an update. PLANTA 2022; 255:50. [PMID: 35084577 DOI: 10.1007/s00425-022-03829-y] [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: 10/29/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
The outcome of different host-pathogen interactions is influenced by both genetic and epigenetic systems, which determine the response of plants to pathogens and vice versa. This review highlights key molecular mechanisms and conceptual advances involved in epigenetic research and the progress made in epigenetics of wheat-rust interactions. Epigenetics implies the heritable changes in the way of gene expression as a consequence of the modification of DNA bases, histone proteins, and/or non-coding-RNA biogenesis without disturbing the underlying nucleotide sequence. The changes occurring between DNA and its surrounding chromatin without altering its DNA sequence and leading to significant changes in the genome of any organism are called epigenetic changes. Epigenetics has already been used successfully to explain the mechanism of human pathogens and in the identification of pathogen-induced modifications within various host plants. Wheat rusts are one of the most vital fungal diseases throughout the major wheat-growing areas of the world. The epigenome in plant pathogens causing diseases such as wheat rusts is mysterious. The investigations of host and pathogen epigenetics in the wheat rusts system can offer a piece of suitable evidence for elucidation of the molecular basis of host-pathogen interaction. Besides, the information on the epigenetic regulation of the genes involved in resistance or pathogenicity will provide better insights into the complex resistance signaling pathways and could provide answers to certain key questions, such as whether epigenetic regulation of certain genes is imparting resistance to host in response of certain pathogen elicitors or not. In the last few years, there has been an upsurge in research on the host as well as pathogen epigenetics and its outcome in plant-pathogen interactions. This review summarizes the progress made in the areas related to the epigenetic control of host-pathogen interaction with particular emphasis on wheat rusts.
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Affiliation(s)
- Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India.
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India.
| | - O P Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
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5
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Werghi S, Herrero FA, Fakhfakh H, Gorsane F. Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato. Gene 2021; 804:145905. [PMID: 34411646 DOI: 10.1016/j.gene.2021.145905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Tomato spotted wilt virus (TSWV) causes severe losses of tomato crops worldwide. To cope dynamically with such a threat, plants deploy strategies acting at the molecular and the epigenetic levels. We found that tomato symptoms progress in a specific-genotype-manner upon TSWV infection. Susceptible genotypes showed within the Auxin Response Factor (ARF8) promoter coupled to enhanced expression of miRNA167a, reduced ARF8 gene and decreased levels of the hormone auxin. This constitutes a deliberate attempt of TSWV to disrupt plant growth to promote spread in sensitive cultivars. Epigenetic regulation through the level of cytosine methylation and the miR167a-ARF8 module are part of a complex network modulating auxin-triggered synthesis and shaping tomato responses to TSWV. Furthermore, modulation of miR167a-ARF8 regulatory module could be applied in tomato-resistance breeding programs.
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Affiliation(s)
- Sirine Werghi
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Frederic Aparicio Herrero
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Valencia 46022, Spain; Dept of Biotechnology, ETSIAMN, Universidad Politécnica de Valencia, 46002, Spain
| | - Hatem Fakhfakh
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia
| | - Faten Gorsane
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia.
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6
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Aggarwal DD, Rybnikov S, Sapielkin S, Rashkovetsky E, Frenkel Z, Singh M, Michalak P, Korol AB. Seasonal changes in recombination characteristics in a natural population of Drosophila melanogaster. Heredity (Edinb) 2021; 127:278-287. [PMID: 34163036 PMCID: PMC8405755 DOI: 10.1038/s41437-021-00449-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Environmental seasonality is a potent evolutionary force, capable of maintaining polymorphism, promoting phenotypic plasticity and causing bet-hedging. In Drosophila, environmental seasonality has been reported to affect life-history traits, tolerance to abiotic stressors and immunity. Oscillations in frequencies of alleles underlying fitness-related traits were also documented alongside SNPs across the genome. Here, we test for seasonal changes in two recombination characteristics, crossover rate and crossover interference, in a natural D. melanogaster population from India using morphological markers of the three major chromosomes. We show that winter flies, collected after the dry season, have significantly higher desiccation tolerance than their autumn counterparts. This difference proved to hold also for hybrids with three independent marker stocks, suggesting its genetic rather than plastic nature. Significant between-season changes are documented for crossover rate (in 9 of 13 studied intervals) and crossover interference (in four of eight studied pairs of intervals); both single and double crossovers were usually more frequent in the winter cohort. The winter flies also display weaker plasticity of both recombination characteristics to desiccation. We ascribe the observed differences to indirect selection on recombination caused by directional selection on desiccation tolerance. Our findings suggest that changes in recombination characteristics can arise even after a short period of seasonal adaptation (~8-10 generations).
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Affiliation(s)
- Dau Dayal Aggarwal
- Department of Zoology, Banaras Hindu University, Varanasi, India.
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.
| | - Sviatoslav Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
| | - Shaul Sapielkin
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Manvender Singh
- Department of Biotechnology, UIET, MD University, Rohtak, India
| | - Pawel Michalak
- Institute of Evolution, University of Haifa, Haifa, Israel
- Edward Via College of Osteopathic Medicine, Monroe, LA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
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7
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Zhang Z, He C, Chen Y, Li B, Tian S. DNA Methyltransferases Regulate Pathogenicity of Botrytis cinerea to Horticultural Crops. J Fungi (Basel) 2021; 7:jof7080659. [PMID: 34436198 PMCID: PMC8399656 DOI: 10.3390/jof7080659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Botrytis cinerea is one of the most destructive fungal pathogens that cause gray mold rot in horticultural products, including fresh fruits, vegetables, and flowers, leading to serious economic losses. B. cinerea is difficult to control because it has strong stress resistance and complex infection modes. The pathogenic mechanisms of B. cinerea have been revealed at multiple levels, but little is known at the epigenetic level. In this study, we first revealed the important role of DNA methyltransferases in regulating the development and pathogenicity of B. cinerea. We showed that two DNA methyltransferases, BcDIM2 and BcRID2, showed a strong synergistic effect in regulating the pathogenicity of B. cinerea. The double knockout mutant ΔBcdim2rid2 showed slower mycelial growth, lower spore germination, attenuated oxidative tolerance, and complete pathogenicity loss on various hosts, which is related to the reduced expression of virulence-related genes in ΔBcdim2rid2 and the induced resistance of the host. Although B. cinerea has multiple DNA methyltransferases, the global methylation level is very low, and few 5mC sites can be detected by BS-seq. These results first revealed the important role and the action mode of DNA methyltransferases in B. cinerea.
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Affiliation(s)
- Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Z.); (C.H.); (Y.C.); (B.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang He
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Z.); (C.H.); (Y.C.); (B.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Z.); (C.H.); (Y.C.); (B.L.)
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Z.); (C.H.); (Y.C.); (B.L.)
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (Z.Z.); (C.H.); (Y.C.); (B.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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8
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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9
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Annacondia ML, Markovic D, Reig-Valiente JL, Scaltsoyiannes V, Pieterse CMJ, Ninkovic V, Slotkin RK, Martinez G. Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:1185-1200. [PMID: 33475147 DOI: 10.1111/nph.17226] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/14/2021] [Indexed: 05/23/2023]
Abstract
Environmentally induced changes in the epigenome help individuals to quickly adapt to fluctuations in the conditions of their habitats. We explored those changes in Arabidopsis thaliana plants subjected to multiple biotic and abiotic stresses, and identified transposable element (TE) activation in plants infested with the green peach aphid, Myzus persicae. We performed a genome-wide analysis mRNA expression, small RNA accumulation and DNA methylation Our results demonstrate that aphid feeding induces loss of methylation of hundreds of loci, mainly TEs. This loss of methylation has the potential to regulate gene expression and we found evidence that it is involved in the control of plant immunity genes. Accordingly, mutant plants deficient in DNA and H3K9 methylation (kyp) showed increased resistance to M. persicae infestation. Collectively, our results show that changes in DNA methylation play a significant role in the regulation of the plant transcriptional response and induction of defense response against aphid feeding.
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Affiliation(s)
- Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Dimitrije Markovic
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
- Faculty of Agriculture, University of Banja Luka, Banja Luka, 78000, Bosnia and Herzegovina
| | - Juan Luis Reig-Valiente
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Vassilis Scaltsoyiannes
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institut de Biologie de Moléculaire des Plantes, UPR 2357 du CNRS, Strasbourg University, Strasbourg, 67000, France
| | - Corné M J Pieterse
- Department of Biology, Science4Life, Utrecht University, Utrecht, 3584 CS, the Netherlands
| | - Velemir Ninkovic
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65021, USA
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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10
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Kumar S, Mohapatra T. Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:596236. [PMID: 34093600 PMCID: PMC8175986 DOI: 10.3389/fpls.2021.596236] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/19/2021] [Indexed: 05/20/2023]
Abstract
Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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11
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Ludovici GM, Oliveira de Souza S, Chierici A, Cascone MG, d'Errico F, Malizia A. Adaptation to ionizing radiation of higher plants: From environmental radioactivity to chernobyl disaster. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 222:106375. [PMID: 32791372 DOI: 10.1016/j.jenvrad.2020.106375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
The purpose of this work is to highlight the effects of ionizing radiation on the genetic material in higher plants by assessing both adaptive processes as well as the evolution of plant species. The effects that the ionizing radiation has on greenery following a nuclear accident, was examined by taking the Chernobyl Nuclear Power Plant disaster as a case study. The genetic and evolutionary effects that ionizing radiation had on plants after the Chernobyl accident were highlighted. The response of biota to Chernobyl irradiation was a complex interaction among radiation dose, dose rate, temporal and spatial variation, varying radiation sensitivities of the different plants' species, and indirect effects from other events. Ionizing radiation causes water radiolysis, generating highly reactive oxygen species (ROS). ROS induce the rapid activation of detoxifying enzymes. DeoxyriboNucleic Acid (DNA) is the object of an attack by both, the hydroxyl ions and the radiation itself, thus triggering a mechanism both direct and indirect. The effects on DNA are harmful to the organism and the long-term development of the species. Dose-dependent aberrations in chromosomes are often observed after irradiation. Although multiple DNA repair mechanisms exist, double-strand breaks (DSBs or DNA-DSBs) are often subject to errors. Plants DSBs repair mechanisms mainly involve homologous and non-homologous dependent systems, the latter especially causing a loss of genetic information. Repeated ionizing radiation (acute or chronic) ensures that plants adapt, demonstrating radioresistance. An adaptive response has been suggested for this phenomenon. As a result, ionizing radiation influences the genetic structure, especially during chronic irradiation, reducing genetic variability. This reduction may be associated with the fact that particular plant species are more subject to chronic stress, confirming the adaptive theory. Therefore, the genomic effects of ionizing radiation demonstrate their likely involvement in the evolution of plant species.
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Affiliation(s)
| | | | - Andrea Chierici
- Department of Industrial Engineering, University of Rome Tor Vergata, Italy; Department of Civil and Industrial Engineering, University of Pisa, Italy
| | | | - Francesco d'Errico
- Department of Civil and Industrial Engineering, University of Pisa, Italy
| | - Andrea Malizia
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Italy.
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12
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Meng WL, Zhao MJ, Yang XB, Zhang AX, Wang NN, Xu ZS, Ma J. Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination. Genes (Basel) 2020; 11:genes11020199. [PMID: 32075264 PMCID: PMC7073617 DOI: 10.3390/genes11020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
Interspecific hybridization creates genetic variation useful for crop improvement. However, whether pollen from a different genus affects the genomic stability and/or transcriptome of the recipient species during intergeneric pollination has not been investigated. Here, we crossed japonica rice cv. Z12 with the maize accession B73 (pollen donor) and obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number, and increased grain weight compared with Z12. To reveal the genetic basis of these morphological changes in MU1, we performed whole-genome resequencing of MU1 and Z12. Compared with Z12, MU1 showed 107,250 single nucleotide polymorphisms (SNPs) and 23,278 insertion/deletions (InDels). Additionally, 5'-upstream regulatory regions (5'UTRs) of 429 and 309 differentially expressed genes (DEGs) in MU1 contained SNPs and InDels, respectively, suggesting that a subset of these DEGs account for the variation in 5'UTRs. Transcriptome analysis revealed 2190 DEGs in MU1 compared with Z12. Genes up-regulated in MU1 were mainly involved in photosynthesis, generation of precursor metabolites, and energy and cellular biosynthetic processes; whereas those down-regulated in MU1 were involved in plant hormone signal transduction pathway and response to stimuli and stress processes. Quantitative PCR (qPCR) further identified the expression levels of the up- or down-regulated gene in plant hormone signal transduction pathway. The expression level changes of plant hormone signal transduction pathway may be significant for plant growth and development. These findings suggest that mutations caused by intergeneric pollination could be the important reason for changes of MU1 in agronomic traits.
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Affiliation(s)
- Wei-Long Meng
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Meng-Jie Zhao
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
| | - Xiang-Bo Yang
- College of Agronomy, Jilin Agricultural Science and Technology University, Jilin 132101, China;
| | - An-Xing Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Ning-Ning Wang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
| | - Zhao-Shi Xu
- Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China;
- Correspondence: (Z.-S.X.); (J.M.)
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (W.-L.M.); (A.-X.Z.); (N.-N.W.)
- Correspondence: (Z.-S.X.); (J.M.)
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13
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González R, Butković A, Elena SF. From foes to friends: Viral infections expand the limits of host phenotypic plasticity. Adv Virus Res 2020; 106:85-121. [PMID: 32327149 DOI: 10.1016/bs.aivir.2020.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain; The Santa Fe Institute, Santa Fe, NM, United States.
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14
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Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
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Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
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15
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Wang C, Wang C, Zou J, Yang Y, Li Z, Zhu S. Epigenetics in the plant-virus interaction. PLANT CELL REPORTS 2019; 38:1031-1038. [PMID: 31065780 DOI: 10.1007/s00299-019-02414-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/25/2019] [Indexed: 05/23/2023]
Abstract
Plants have developed diverse molecular mechanisms to resist viruses. RNA silencing plays a dominant role in antiviral defense. Recent studies have correlated plant antiviral silencing to epigenetic modification in genomic DNA and protein by remodeling the expression levels of coding genes. The plant host methylation level is reprogrammed in response to viral challenge. Genomes of some viruses have been implicated in the epigenetic modification via small RNA-mediated transcriptional gene silencing and post-transcriptional gene silencing. These mechanisms can be primed prior to a virus attack through methylation changes for antiviral defense. This review highlights the findings concerning the methylation changes in plant-virus interactions and demonstrates a possible direction to improve the understanding of plant host methylation regulation in response to viral infection.
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Affiliation(s)
- Chenguang Wang
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Chaonan Wang
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Jingze Zou
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Yunshu Yang
- Beijing Academy of Food Sciences, Beijing, 100162, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Shuifang Zhu
- College of Plant Protection, China Agricultural University, Beijing, 100083, China.
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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16
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Liégard B, Baillet V, Etcheverry M, Joseph E, Lariagon C, Lemoine J, Evrard A, Colot V, Gravot A, Manzanares‐Dauleux MJ, Jubault M. Quantitative resistance to clubroot infection mediated by transgenerational epigenetic variation in Arabidopsis. THE NEW PHYTOLOGIST 2019; 222:468-479. [PMID: 30393890 PMCID: PMC6587750 DOI: 10.1111/nph.15579] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/26/2018] [Indexed: 05/02/2023]
Abstract
Quantitative disease resistance, often influenced by environmental factors, is thought to be the result of DNA sequence variants segregating at multiple loci. However, heritable differences in DNA methylation, so-called transgenerational epigenetic variants, also could contribute to quantitative traits. Here, we tested this possibility using the well-characterized quantitative resistance of Arabidopsis to clubroot, a Brassica major disease caused by Plasmodiophora brassicae. For that, we used the epigenetic recombinant inbred lines (epiRIL) derived from the cross ddm1-2 × Col-0, which show extensive epigenetic variation but limited DNA sequence variation. Quantitative loci under epigenetic control (QTLepi ) mapping was carried out on 123 epiRIL infected with P. brassicae and using various disease-related traits. EpiRIL displayed a wide range of continuous phenotypic responses. Twenty QTLepi were detected across the five chromosomes, with a bona fide epigenetic origin for 16 of them. The effect of five QTLepi was dependent on temperature conditions. Six QTLepi co-localized with previously identified clubroot resistance genes and QTL in Arabidopsis. Co-localization of clubroot resistance QTLepi with previously detected DNA-based QTL reveals a complex model in which a combination of allelic and epiallelic variations interacts with the environment to lead to variation in clubroot quantitative resistance.
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Affiliation(s)
- Benjamin Liégard
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
| | - Victoire Baillet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Ecole Normale SupérieureCentre National de la Recherche Scientifique (CNRS)Institut National de la Santé et de la Recherche Médicale (INSERM)F‐75005ParisFrance
| | - Mathilde Etcheverry
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Ecole Normale SupérieureCentre National de la Recherche Scientifique (CNRS)Institut National de la Santé et de la Recherche Médicale (INSERM)F‐75005ParisFrance
| | - Evens Joseph
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
| | | | - Jocelyne Lemoine
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
| | - Aurélie Evrard
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Ecole Normale SupérieureCentre National de la Recherche Scientifique (CNRS)Institut National de la Santé et de la Recherche Médicale (INSERM)F‐75005ParisFrance
| | - Antoine Gravot
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
| | | | - Mélanie Jubault
- IGEPPINRAAGROCAMPUS OUESTUniversité de RennesF‐35000RennesFrance
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17
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Dutta S, Mitra M, Agarwal P, Mahapatra K, De S, Sett U, Roy S. Oxidative and genotoxic damages in plants in response to heavy metal stress and maintenance of genome stability. PLANT SIGNALING & BEHAVIOR 2018; 13:e1460048. [PMID: 29621424 PMCID: PMC6149466 DOI: 10.1080/15592324.2018.1460048] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/28/2018] [Indexed: 05/17/2023]
Abstract
Plants, being sessile in nature, are constantly exposed to various environmental stresses, such as solar UV radiations, soil salinity, drought and desiccation, rehydration, low and high temperatures and other vast array of air and soil borne chemicals, industrial waste products, metals and metalloids. These agents, either directly or indirectly via the induction of oxidative stress and overproduction of reactive oxygen species (ROS), frequently perturb the chemical or physical structures of DNA and induce both cytotoxic or genotoxic stresses. Such condition, in turn, leads to genome instability and thus eventually severely affecting plant health and crop yield. With the growing industrialization process and non-judicious use of chemical fertilizers, the heavy metal mediated chemical toxicity has become one of the major environmental threats for the plants around the globe. The heavy metal ions cause damage to the structural, enzymatic and non-enzymatic components of plant cell, often resulting in loss of cell viability, thus negatively impacting plant growth and development. Plants have also evolved with an extensive and highly efficient mechanism to respond and adapt under such heavy metal toxicity mediated stress conditions. In addition to morpho-anatomical, hormonal and biochemical responses, at the molecular level, plants respond to heavy metal stress induced oxidative and genotoxic damage via the rapid change in the expression of the responsive genes at the transcriptional level. Various families of transcription factors play crucial role in triggering such responses. Apart from transcriptional response, epigenetic modifications have also been found to be essential for maintenance of plant genome stability under genotoxic stress. This review represents a comprehensive survey of recent advances in our understanding of plant responses to heavy metal mediated toxicity in general with particular emphasis on the transcriptional and epigenetic responses and highlights the importance of understanding the potential targets in the associated pathways for improved stress tolerance in crops.
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Affiliation(s)
- Subhajit Dutta
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Mehali Mitra
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Puja Agarwal
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Kalyan Mahapatra
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Sayanti De
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Upasana Sett
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Centre of Advanced Studies, The University of Burdwan, Golapbag campus, Burdwan – 713104, West Bengal, India
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18
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Hu J, Pérez-Jvostov F, Blondel L, Barrett RDH. Genome-wide DNA methylation signatures of infection status in Trinidadian guppies (Poecilia reticulata
). Mol Ecol 2018; 27:3087-3102. [DOI: 10.1111/mec.14771] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Juntao Hu
- Redpath Museum; McGill University; Montreal Quebec Canada
- Department of Biology; McGill University; Montreal Quebec Canada
| | - Felipe Pérez-Jvostov
- Redpath Museum; McGill University; Montreal Quebec Canada
- Department of Biology; McGill University; Montreal Quebec Canada
| | - Léa Blondel
- Redpath Museum; McGill University; Montreal Quebec Canada
- Department of Biology; McGill University; Montreal Quebec Canada
| | - Rowan D. H. Barrett
- Redpath Museum; McGill University; Montreal Quebec Canada
- Department of Biology; McGill University; Montreal Quebec Canada
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19
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20
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Dalio RJD, Máximo HJ, Oliveira TS, Azevedo TDM, Felizatti HL, Campos MDA, Machado MA. Molecular Basis of Citrus sunki Susceptibility and Poncirus trifoliata Resistance Upon Phytophthora parasitica Attack. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:386-398. [PMID: 29125028 DOI: 10.1094/mpmi-05-17-0112-fi] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Coevolution has shaped the molecular basis of an extensive number of defense mechanisms in plant-pathogen interactions. Phytophthora parasitica, a hemibiothrophic oomycete pathogen and the causal agent of citrus root rot and gummosis, interacts differently with Citrus sunki and Poncirus trifoliata, two commonly favored citrus rootstocks that are recognized as susceptible and resistant, respectively, to P. parasitica. The molecular core of these interactions remains elusive. Here, we provide evidence on the defense strategies employed by both susceptible and resistant citrus rootstocks, in parallel with P. parasitica deployment of effectors. Time course expression analysis (quantitative real-time polymerase chain reaction) of several defense-related genes were evaluated during i) plant disease development, ii) necrosis, and iii) pathogen effector gene expression. In C. sunki, P. parasitica deploys effectors, including elicitins, NPP1 (necrosis-inducing Phytophthora protein 1), CBEL (cellulose-binding elicitor and lectin activity), RxLR, and CRN (crinkler), and, consequently, this susceptible plant activates its main defense signaling pathways that result in the hypersensitive response and necrosis. Despite the strong plant-defense response, it fails to withstand P. parasitica invasion, confirming its hemibiothrophic lifestyle. In Poncirus trifoliata, the effectors were strongly expressed, nevertheless failing to induce any immunity manipulation and disease development, suggesting a nonhost resistance type, in which the plant relies on preformed biochemical and anatomical barriers.
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Affiliation(s)
| | - Heros José Máximo
- 1 Biotechnology Lab, Centro de Citricultura Sylvio Moreira. Cordeirópolis-SP, Brazil
| | - Tiago Silva Oliveira
- 1 Biotechnology Lab, Centro de Citricultura Sylvio Moreira. Cordeirópolis-SP, Brazil
| | | | - Henrique Leme Felizatti
- 2 Instituto de Matemática, Estatística e Computação Científica, Universidade de Campinas, Campinas-SP, Brazil; and
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21
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Cortez MJV, Rabajante JF, Tubay JM, Babierra AL. From epigenetic landscape to phenotypic fitness landscape: Evolutionary effect of pathogens on host traits. INFECTION GENETICS AND EVOLUTION 2017; 51:245-254. [PMID: 28408285 DOI: 10.1016/j.meegid.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate the association between the epigenetic and phenotypic fitness landscapes and how parasitism facilitates non-genetic phenotypic diversity.
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Affiliation(s)
- Mark Jayson V Cortez
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Jomar F Rabajante
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines.
| | - Jerrold M Tubay
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Ariel L Babierra
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
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22
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Castellano M, Martinez G, Marques MC, Moreno-Romero J, Köhler C, Pallas V, Gomez G. Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5857-5868. [PMID: 27697787 PMCID: PMC5066502 DOI: 10.1093/jxb/erw353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Eukaryotic organisms exposed to adverse conditions are required to show a certain degree of transcriptional plasticity in order to cope successfully with stress. Epigenetic regulation of the genome is a key regulatory mechanism allowing dynamic changes of the transcriptional status of the plant in response to stress. The Hop stunt viroid (HSVd) induces the demethylation of ribosomal RNA (rRNA) in cucumber (Cucumis sativus) leaves, leading to increasing transcription rates of rRNA. In addition to the clear alterations observed in vegetative tissues, HSVd infection is also associated with drastic changes in gametophyte development. To examine the basis of viroid-induced alterations in reproductive tissues, we analysed the cellular and molecular consequences of HSVd infection in the male gametophyte of cucumber plants. Our results indicate that in the pollen grain, accumulation of HSVd RNA induces a decondensation of the generative nucleus that correlates with a dynamic demethylation of repetitive regions in the cucumber genome that include rRNA genes and transposable elements (TEs). We therefore propose that HSVd infection impairs the epigenetic control of rRNA genes and TEs in gametic cells of cucumber, a phenomenon thus far unknown to occur in this reproductive tissue as a consequence of pathogen infection.
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Affiliation(s)
- Mayte Castellano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Maria Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Gustavo Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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23
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Bordiya Y, Zheng Y, Nam JC, Bonnard AC, Choi HW, Lee BK, Kim J, Klessig DF, Fei Z, Kang HG. Pathogen Infection and MORC Proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:674-687. [PMID: 27482822 DOI: 10.1094/mpmi-01-16-0023-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To assess the role of MORC1 in epigenetics in relation to plant immunity, genome-wide chromatin accessibility was compared between mock- or Pseudomonas syringae pv. tomato-inoculated wild type (WT) Arabidopsis, the morc1/2 double mutant, or both. Most changes in chromatin accessibility, scored by DNase I hypersensitive sites (DHSs), were located in the promoters of genes and transposable elements (TEs). Comparisons between morc1/2 and WT receiving the same treatment revealed differential DHSs (dDHSs) predominantly associated with heterochromatic TEs. By contrast, comparisons between mock- and P. syringae pv. tomato-inoculated plants from the same genotype showed dDHSs associated with biotic and abiotic stress-related genes; a smaller but significant population was in TEs. Moreover, many defense genes, including PR-1, PR-2, and PR-5, were proximal to P. syringae pv. tomato-induced, TE-associated dDHSs. A random subset of these defense genes showed moderately delayed or reduced expression or both in P. syringae pv. tomato-infected morc1/2 as compared with WT. MORC1 was physically bound to chromatin in a P. syringae pv. tomato infection-responsive manner at sites dispersed throughout the genome. Notably, silencing of TE-associated dDHSs proximal to these infection-induced, MORC1-interacting sites led to significant suppression of P. syringae pv. tomato-induced transcription of adjacent defense genes, including PR-1. These results provide evidence that MORC1 is associated with TEs and suggest that a subset of these TEs may help regulate their proximal defense genes.
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Affiliation(s)
- Yogendra Bordiya
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - Yi Zheng
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Ji-Chul Nam
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - April C Bonnard
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
| | - Hyong Woo Choi
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Bum-Kyu Lee
- 3 Department of Molecular Biosciences, The University of Texas at Austin, U.S.A.; and
| | - Jonghwan Kim
- 3 Department of Molecular Biosciences, The University of Texas at Austin, U.S.A.; and
| | - Daniel F Klessig
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
| | - Zhangjun Fei
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY, U.S.A
- 4 USDA Robert W. Holley Center for Agriculture and Health, Tower Road, Ithaca, NY, U.S.A
| | - Hong-Gu Kang
- 1 Department of Biology, Texas State University, San Marcos, TX, U.S.A
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24
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Niehl A, Wyrsch I, Boller T, Heinlein M. Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants. THE NEW PHYTOLOGIST 2016; 211:1008-19. [PMID: 27030513 DOI: 10.1111/nph.13944] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 05/20/2023]
Abstract
Pattern-triggered immunity (PTI) is a plant defense response that relies on the perception of conserved microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs, respectively). Recently, it has been recognized that PTI restricts virus infection in plants; however, the nature of the viral or infection-induced PTI elicitors and the underlying signaling pathways are still unknown. As double-stranded RNAs (dsRNAs) are conserved molecular patterns associated with virus replication, we applied dsRNAs or synthetic dsRNA analogs to Arabidopsis thaliana and investigated PTI responses. We show that in vitro-generated dsRNAs, dsRNAs purified from virus-infected plants and the dsRNA analog polyinosinic-polycytidylic acid (poly(I:C)) induce typical PTI responses dependent on the co-receptor SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1 (SERK1), but independent of dicer-like (DCL) proteins in Arabidopsis. Moreover, dsRNA treatment of Arabidopsis induces SERK1-dependent antiviral resistance. Screening of Arabidopsis wild accessions demonstrates natural variability in dsRNA sensitivity. Our findings suggest that dsRNAs represent genuine PAMPs in plants, which induce a signaling cascade involving SERK1 and a specific dsRNA receptor. The dependence of dsRNA-mediated PTI on SERK1, but not on DCLs, implies that dsRNA-mediated PTI involves membrane-associated processes and operates independently of RNA silencing. dsRNA sensitivity may represent a useful trait to increase antiviral resistance in cultivated plants.
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Affiliation(s)
- Annette Niehl
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Ines Wyrsch
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Thomas Boller
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
| | - Manfred Heinlein
- Botany, Department of Environmental Sciences, University of Basel, Basel, CH-4056, Switzerland
- Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Strasbourg, 67000, France
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Manova V, Gruszka D. DNA damage and repair in plants - from models to crops. FRONTIERS IN PLANT SCIENCE 2015; 6:885. [PMID: 26557130 PMCID: PMC4617055 DOI: 10.3389/fpls.2015.00885] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 10/05/2015] [Indexed: 05/17/2023]
Abstract
The genomic integrity of every organism is constantly challenged by endogenous and exogenous DNA-damaging factors. Mutagenic agents cause reduced stability of plant genome and have a deleterious effect on development, and in the case of crop species lead to yield reduction. It is crucial for all organisms, including plants, to develop efficient mechanisms for maintenance of the genome integrity. DNA repair processes have been characterized in bacterial, fungal, and mammalian model systems. The description of these processes in plants, in contrast, was initiated relatively recently and has been focused largely on the model plant Arabidopsis thaliana. Consequently, our knowledge about DNA repair in plant genomes - particularly in the genomes of crop plants - is by far more limited. However, the relatively small size of the Arabidopsis genome, its rapid life cycle and availability of various transformation methods make this species an attractive model for the study of eukaryotic DNA repair mechanisms and mutagenesis. Moreover, abnormalities in DNA repair which proved to be lethal for animal models are tolerated in plant genomes, although sensitivity to DNA damaging agents is retained. Due to the high conservation of DNA repair processes and factors mediating them among eukaryotes, genes and proteins that have been identified in model species may serve to identify homologous sequences in other species, including crop plants, in which these mechanisms are poorly understood. Crop breeding programs have provided remarkable advances in food quality and yield over the last century. Although the human population is predicted to "peak" by 2050, further advances in yield will be required to feed this population. Breeding requires genetic diversity. The biological impact of any mutagenic agent used for the creation of genetic diversity depends on the chemical nature of the induced lesions and on the efficiency and accuracy of their repair. More recent targeted mutagenesis procedures also depend on host repair processes, with different pathways yielding different products. Enhanced understanding of DNA repair processes in plants will inform and accelerate the engineering of crop genomes via both traditional and targeted approaches.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of SciencesSofia
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of SilesiaKatowice, Poland
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The DNA damage response and immune signaling alliance: Is it good or bad? Nature decides when and where. Pharmacol Ther 2015; 154:36-56. [PMID: 26145166 DOI: 10.1016/j.pharmthera.2015.06.011] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 12/15/2022]
Abstract
The characteristic feature of healthy living organisms is the preservation of homeostasis. Compelling evidence highlight that the DNA damage response and repair (DDR/R) and immune response (ImmR) signaling networks work together favoring the harmonized function of (multi)cellular organisms. DNA and RNA viruses activate the DDR/R machinery in the host cells both directly and indirectly. Activation of DDR/R in turn favors the immunogenicity of the incipient cell. Hence, stimulation of DDR/R by exogenous or endogenous insults triggers innate and adaptive ImmR. The immunogenic properties of ionizing radiation, a prototypic DDR/R inducer, serve as suitable examples of how DDR/R stimulation alerts host immunity. Thus, critical cellular danger signals stimulate defense at the systemic level and vice versa. Disruption of DDR/R-ImmR cross talk compromises (multi)cellular integrity, leading to cell-cycle-related and immune defects. The emerging DDR/R-ImmR concept opens up a new avenue of therapeutic options, recalling the Hippocrates quote "everything in excess is opposed by nature."
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Dawson IK, Russell J, Powell W, Steffenson B, Thomas WTB, Waugh R. Barley: a translational model for adaptation to climate change. THE NEW PHYTOLOGIST 2015; 206:913-931. [PMID: 25605349 DOI: 10.1111/nph.13266] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.
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Affiliation(s)
- Ian K Dawson
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Wayne Powell
- CGIAR Consortium Office, Montpellier Cedex 5, France
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - William T B Thomas
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, College of Life Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
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Abstract
The genetic enhancement of wild animals and plants for characteristics that benefit human populations has been practiced for thousands of years, resulting in impressive improvements in commercially valuable species. Despite these benefits, genetic manipulations are rarely considered for noncommercial purposes, such as conservation and restoration initiatives. Over the last century, humans have driven global climate change through industrialization and the release of increasing amounts of CO2, resulting in shifts in ocean temperature, ocean chemistry, and sea level, as well as increasing frequency of storms, all of which can profoundly impact marine ecosystems. Coral reefs are highly diverse ecosystems that have suffered massive declines in health and abundance as a result of these and other direct anthropogenic disturbances. There is great concern that the high rates, magnitudes, and complexity of environmental change are overwhelming the intrinsic capacity of corals to adapt and survive. Although it is important to address the root causes of changing climate, it is also prudent to explore the potential to augment the capacity of reef organisms to tolerate stress and to facilitate recovery after disturbances. Here, we review the risks and benefits of the improvement of natural and commercial stocks in noncoral reef systems and advocate a series of experiments to determine the feasibility of developing coral stocks with enhanced stress tolerance through the acceleration of naturally occurring processes, an approach known as (human)-assisted evolution, while at the same time initiating a public dialogue on the risks and benefits of this approach.
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Rodríguez López CM, Wilkinson MJ. Epi-fingerprinting and epi-interventions for improved crop production and food quality. FRONTIERS IN PLANT SCIENCE 2015; 6:397. [PMID: 26097484 PMCID: PMC4456566 DOI: 10.3389/fpls.2015.00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/18/2015] [Indexed: 05/05/2023]
Abstract
Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.
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Affiliation(s)
- Carlos M. Rodríguez López
- *Correspondence: Carlos M. Rodríguez López, Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, Adelaide, SA 5064, Australia
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Arnholdt-Schmitt B, Valadas V, Döring M. Functional marker development is challenged by the ubiquity of endophytes-a practical perspective. Brief Funct Genomics 2014; 15:16-21. [PMID: 25526729 DOI: 10.1093/bfgp/elu049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Functional markers (FMs) are supposed to assist in diagnosis, disease treatment and turning plant and animal breeding more efficient. However, efficient FM application is challenged through current insights in the multi-organism nature of life. This letter aims to raise awareness for re-thinking concepts for FM development in plant breeding and proposes a novel perspective.
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Tang XM, Tao X, Wang Y, Ma DW, Li D, Yang H, Ma XR. Analysis of DNA methylation of perennial ryegrass under drought using the methylation-sensitive amplification polymorphism (MSAP) technique. Mol Genet Genomics 2014; 289:1075-84. [PMID: 24916310 DOI: 10.1007/s00438-014-0869-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022]
Abstract
Perennial ryegrass (Lolium perenne), an excellent grass for forage and turf, is widespread in temperate regions. Drought is an important factor that limits its growth, distribution, and yield. DNA methylation affects gene expression and plays an important role in adaptation to adverse environments. In this study, the DNA methylation changes in perennial ryegrass under drought stress were assessed using methylation-sensitive amplified polymorphism (MSAP). After 15 days of drought stress treatment, the plant height was less than half of the control, and the leaves were smaller and darker. Genome-wide, a total of 652 CCGG sites were detected by MSAP. The total methylation level was 57.67 and 47.39 % in the control and drought treatment, respectively, indicating a decrease of 10.28 % due to drought exposure. Fifteen differentially displayed DNA fragments in MSAP profiles were cloned for sequencing analysis. The results showed that most of the genes involved in stress responses. The relative expression levels revealed that three demethylated fragments were up-regulated. The expression of a predicted retrotransposon increased significantly, changing from hypermethylation to non-methylation. Although the extent of methylation in two other genes decreased, the sites of methylation remained, and the expression increased only slightly. All of these results suggested that drought stress decreased the total DNA methylation level in perennial ryegrass and demethylation up-regulated related gene expressions and that the extent of methylation was negatively correlated with expression. Overall, the induced epigenetic changes in genome probably are an important regulatory mechanism for acclimating perennial ryegrass to drought and possibly other environmental stresses.
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Affiliation(s)
- Xiao-Mei Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No 9, Section 4, Renmin South Road, Chengdu, 610041, China
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Bilichak A, Yao Y, Titov V, Golubov A, Kovalchuk I. Genome stability in the uvh6 mutant of Arabidopsis thaliana. PLANT CELL REPORTS 2014; 33:979-991. [PMID: 24553752 DOI: 10.1007/s00299-014-1580-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/21/2014] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
Plant XPD homolog UVH6 is the protein involved in the repair of strand breaks, and the excision repair and uvh6 mutant is not impaired in transgenerational increase in HRF. While analyzing the transgenerational response to stress in plants, we found that the promoter and gene body of Arabidopsis thaliana (Arabidopsis) XPD homolog UVH6 underwent hypomethylation and showed an increase in the level of transcript. Here, we analyzed the mutant of this gene, uvh6-1, by crossing it to two different reporter lines: one which allows for analysis of homologous recombination frequency (HRF) and another which makes it possible to analyze the frequency of point mutations. We observed that uvh6-1 plants exhibited lower rate of spontaneous homologous recombination but higher frequencies of spontaneous point mutations. The analysis of strand breaks using ROPS and Comet assays showed that the mutant had a much higher level of strand breaks at non-induced conditions. Exposure to stresses such as UVC, heat, cold, flood and drought showed that the mutant was not impaired in an increase in somatic HRF. The analysis of spontaneous HRF in the progeny of control plants compared to that of the progeny of stressed plants demonstrated that uvh6-1 was mildly affected in response to temperature, UV and drought. Our data suggest that UVH6 may be involved in the repair of strand breaks and excision repair, but it is unlikely that UVH6 is required for transgenerational increase in HRF.
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Affiliation(s)
- Andriy Bilichak
- Department of Biological Sciences, University of Lethbridge, University Drive 4401, Lethbridge, AB, T1K 3M4, Canada,
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Cicatelli A, Todeschini V, Lingua G, Biondi S, Torrigiani P, Castiglione S. Epigenetic control of heavy metal stress response in mycorrhizal versus non-mycorrhizal poplar plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1723-1737. [PMID: 23975714 DOI: 10.1007/s11356-013-2072-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
It was previously shown that arbuscular mycorrhizal fungi (AMF) exert a significant improvement of growth in a tolerant white poplar (Populus alba L.) clone (AL35) grown on Cu- and Zn-polluted soil via foliar alterations in the levels of defence/stress-related transcripts and molecules. However, nothing is known about the epigenetic changes which occur during tolerance acquisition in response to heavy metals (HMs) in the same mycorrhizal vs. non-mycorrhizal poplar plants. In order to analyse the epigenome in leaves of AL35 plants inoculated or not with AMF and grown in a greenhouse on multimetal polluted or unpolluted soil, the Methylation Sensitive Amplification Polymorphism (MSAP) approach was adopted to detect cytosine DNA methylation. Modest changes in cytosine methylation patterns were detected at first sampling (4 months from planting), whereas extensive alterations (hypomethylation) occurred at second sampling (after 6 months) in mycorrhizal plants grown in the presence of HMs. The sequencing of MSAP fragments led to the identification of genes belonging to several Gene Ontology categories. Seven MSAP fragments, selected on the basis of DNA methylation status in treated vs control AL35 leaves at the end of the experiment, were analysed for their transcript levels by means of qRT-PCR. Gene expression varied in treated samples relative to controls in response to HMs and/or AMF inoculation; in particular, transcripts of genes involved in RNA processing, cell wall and amino acid metabolism were upregulated in the presence of AMF with or without HMs.
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Affiliation(s)
- Angela Cicatelli
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy
| | - Valeria Todeschini
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Stefania Biondi
- Dipartimento BiGeA, Università di Bologna, 40126, Bologna, Italy
| | - Patrizia Torrigiani
- Dipartimento di Scienze Agrarie, Università di Bologna, 40127, Bologna, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy.
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Király L, Künstler A, Bacsó R, Hafez Y, Király Z. Similarities and differences in plant and animal immune systems — what is inhibiting pathogens? ACTA ACUST UNITED AC 2013. [DOI: 10.1556/aphyt.48.2013.2.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Wang ZH, Zhang D, Bai Y, Zhang YH, Liu Y, Wu Y, Lin XY, Wen JW, Xu CM, Li LF, Liu B. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing. PLoS One 2013; 8:e74479. [PMID: 24058573 PMCID: PMC3776793 DOI: 10.1371/journal.pone.0074479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible species may represent a potent means to generate novel genetic diversities, and which may have played relevant roles in plant evolution and can be manipulated for crop improvements.
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Affiliation(s)
- Zhen-Hui Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Di Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yan Bai
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yun-Hong Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiu-Yun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jia-Wei Wen
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chun-Ming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE) and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- * E-mail: (LL); (BL)
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Donà M, Macovei A, Faè M, Carbonera D, Balestrazzi A. Plant hormone signaling and modulation of DNA repair under stressful conditions. PLANT CELL REPORTS 2013; 32:1043-52. [PMID: 23508254 DOI: 10.1007/s00299-013-1410-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/27/2013] [Accepted: 03/01/2013] [Indexed: 05/08/2023]
Abstract
The role played by phytohormone signaling in the modulation of DNA repair gene and the resulting effects on plant adaptation to genotoxic stress are poorly investigated. Information has been gathered using the Arabidopsis ABA (abscisic acid) overly sensitive mutant abo4-1, defective in the DNA polymerase ε function that is required for DNA repair and recombination. Similarly, phytohormone-mediated regulation of the Ku genes, encoding the Ku heterodimer protein involved in DNA repair, cell cycle control and telomere homeostasis has been demonstrated, highlighting a scenario in which hormones might affect genome stability by modulating the frequency of homologous recombination, favoring plant adaptation to genotoxic stress. Within this context, the characterisation of Arabidopsis AtKu mutants allowed disclosing novel connections between DNA repair and phytohormone networks. Another intriguing aspect deals with the emerging correlation between plant defense response and the mechanisms responsible for genome stability. There is increasing evidence that systemic acquired resistance (SAR) and homologous recombination share common elements represented by proteins involved in DNA repair and chromatin remodeling. This hypothesis is supported by the finding that volatile compounds, such as methyl salicylate (MeSA) and methyl jasmonate (MeJA), participating in the plant-to-plant communication can trigger genome instability in response to genotoxic stress agents. Phytohormone-mediated control of genome stability involves also chromatin remodeling, thus expanding the range of molecular targets. The present review describes the most significant advances in this specific research field, in the attempt to provide a better comprehension of how plant hormones modulate DNA repair proteins as a function of stress.
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Affiliation(s)
- Mattia Donà
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 1, 27100 Pavia, Italy
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Migicovsky Z, Kovalchuk I. Changes to DNA methylation and homologous recombination frequency in the progeny of stressed plants. Biochem Cell Biol 2013; 91:1-5. [PMID: 23442135 DOI: 10.1139/bcb-2012-0046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plants undergo changes in response to biotic and abiotic stresses that help them adjust and survive. Some of these changes may even be passed on to progeny and eventually lead to adaptive evolution. Transgenerational changes in response to stress include alterations in DNA methylation and changes in homologous recombination frequency (HRF). The progeny of plants that were stressed often show elevated HRF as well as genomic hypermethylation, although specific loci that are beneficial in times of stress may be hypomethylated. One of the possible mechanisms responsible for passing the memory to the progeny involves small interfering RNAs; Dicer-like proteins, DCL2 and DCL3, are in part required for this process. However, while epigenetic modifications are often present in the untreated progeny of stressed plants, they are not usually sustained for multiple unexposed generations. Still, transgenerational inheritance of such changes has already begun to provide evidence for an important role of epigenetics in enhancing stress resistance.
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Affiliation(s)
- Zoë Migicovsky
- University of Lethbridge, Department of Biological Sciences, Lethbridge, AB T1K 3M4, Canada
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Michelmore RW, Christopoulou M, Caldwell KS. Impacts of resistance gene genetics, function, and evolution on a durable future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:291-319. [PMID: 23682913 DOI: 10.1146/annurev-phyto-082712-102334] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Studies on resistance gene function and evolution lie at the confluence of structural and molecular biology, genetics, and plant breeding. However, knowledge from these disparate fields has yet to be extensively integrated. This review draws on ideas and information from these different fields to elucidate the influences driving the evolution of different types of resistance genes in plants and the concurrent evolution of virulence in pathogens. It provides an overview of the factors shaping the evolution of recognition, signaling, and response genes in the context of emerging functional information along with a consideration of the new opportunities for durable resistance enabled by high-throughput DNA sequencing technologies.
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Gómez-Díaz E, Jordà M, Peinado MA, Rivero A. Epigenetics of host-pathogen interactions: the road ahead and the road behind. PLoS Pathog 2012; 8:e1003007. [PMID: 23209403 PMCID: PMC3510240 DOI: 10.1371/journal.ppat.1003007] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A growing body of evidence points towards epigenetic mechanisms being responsible for a wide range of biological phenomena, from the plasticity of plant growth and development to the nutritional control of caste determination in honeybees and the etiology of human disease (e.g., cancer). With the (partial) elucidation of the molecular basis of epigenetic variation and the heritability of certain of these changes, the field of evolutionary epigenetics is flourishing. Despite this, the role of epigenetics in shaping host-pathogen interactions has received comparatively little attention. Yet there is plenty of evidence supporting the implication of epigenetic mechanisms in the modulation of the biological interaction between hosts and pathogens. The phenotypic plasticity of many key parasite life-history traits appears to be under epigenetic control. Moreover, pathogen-induced effects in host phenotype may have transgenerational consequences, and the bases of these changes and their heritability probably have an epigenetic component. The significance of epigenetic modifications may, however, go beyond providing a mechanistic basis for host and pathogen plasticity. Epigenetic epidemiology has recently emerged as a promising area for future research on infectious diseases. In addition, the incorporation of epigenetic inheritance and epigenetic plasticity mechanisms to evolutionary models and empirical studies of host-pathogen interactions will provide new insights into the evolution and coevolution of these associations. Here, we review the evidence available for the role epigenetics on host-pathogen interactions, and the utility and versatility of the epigenetic technologies available that can be cross-applied to host-pathogen studies. We conclude with recommendations and directions for future research on the burgeoning field of epigenetics as applied to host-pathogen interactions.
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Affiliation(s)
- Elena Gómez-Díaz
- Institut de Biologia Evolutiva (IBE, CSIC-UPF), Barcelona, Spain
| | - Mireia Jordà
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Spain
| | - Miguel Angel Peinado
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC), Badalona, Spain
| | - Ana Rivero
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC, UMR CNRS-UM2-UM1 5290, IRD 224), Centre IRD, Montpellier, France
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40
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Ou X, Zhang Y, Xu C, Lin X, Zang Q, Zhuang T, Jiang L, von Wettstein D, Liu B. Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.). PLoS One 2012; 7:e41143. [PMID: 22984395 PMCID: PMC3439459 DOI: 10.1371/journal.pone.0041143] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 06/18/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND DNA methylation is sensitive and responsive to stressful environmental conditions. Nonetheless, the extent to which condition-induced somatic methylation modifications can impose transgenerational effects remains to be fully understood. Even less is known about the biological relevance of the induced epigenetic changes for potentially altered well-being of the organismal progenies regarding adaptation to the specific condition their progenitors experienced. METHODOLOGY/PRINCIPAL FINDINGS We analyzed DNA methylation pattern by gel-blotting at genomic loci representing transposable elements and protein-coding genes in leaf-tissue of heavy metal-treated rice (Oryza sativa) plants (S0), and its three successive organismal generations. We assessed expression of putative genes involved in establishing and/or maintaining DNA methylation patterns by reverse transcription (RT)-PCR. We measured growth of the stressed plants and their unstressed progenies vs. the control plants. We found (1) relative to control, DNA methylation patterns were modified in leaf-tissue of the immediately treated plants, and the modifications were exclusively confined to CHG hypomethylation; (2) the CHG-demethylated states were heritable via both maternal and paternal germline, albeit often accompanying further hypomethylation; (3) altered expression of genes encoding for DNA methyltransferases, DNA glycosylase and SWI/SNF chromatin remodeling factor (DDM1) were induced by the stress; (4) progenies of the stressed plants exhibited enhanced tolerance to the same stress their progenitor experienced, and this transgenerational inheritance of the effect of condition accompanying heritability of modified methylation patterns. CONCLUSIONS/SIGNIFICANCE Our findings suggest that stressful environmental condition can produce transgenerational epigenetic modifications. Progenies of stressed plants may develop enhanced adaptability to the condition, and this acquired trait is inheritable and accord with transmission of the epigenetic modifications. We suggest that environmental induction of heritable modifications in DNA methylation provides a plausible molecular underpinning for the still contentious paradigm of inheritance of acquired traits originally put forward by Jean-Baptiste Lamarck more than 200 years ago.
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MESH Headings
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Chromatin/metabolism
- Crosses, Genetic
- DNA Methylation/drug effects
- DNA Methylation/genetics
- DNA Transposable Elements/genetics
- Gene Expression Regulation, Plant/drug effects
- Genetic Loci/genetics
- Hybridization, Genetic
- Inheritance Patterns/genetics
- Metals, Heavy/toxicity
- Open Reading Frames/genetics
- Oryza/drug effects
- Oryza/genetics
- Oryza/growth & development
- Oryza/physiology
- Phenotype
- Quantitative Trait, Heritable
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Seedlings/drug effects
- Seedlings/physiology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
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Affiliation(s)
- Xiufang Ou
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yunhong Zhang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qi Zang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Tingting Zhuang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Diter von Wettstein
- Department of Crop and Soil Sciences and School of Molecular Biology, Washington State University, Pullman, Washington, United States of America
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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41
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Transgenerational defense induction and epigenetic inheritance in plants. Trends Ecol Evol 2012; 27:618-26. [PMID: 22940222 DOI: 10.1016/j.tree.2012.07.011] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/12/2012] [Accepted: 07/15/2012] [Indexed: 11/23/2022]
Abstract
Rapidly accumulating evidence shows that herbivore and pathogen attack of plants can generate particular defense phenotypes across generations. What was once thought to be an oddity of plant defense induction now appears to be a taxonomically widespread phenomenon with strong potential to impact the ecology and evolution of species interactions. DNA methylation, histone modifications, and small RNAs each contribute to transgenerational defense initiation; examples in several species demonstrate that this induction can last for multiple generations. Priming of the offspring generation for more rapid induction following subsequent attack has also been reported. The extent to which transgenerational induction is predictable, detectable in nature, and subject to manipulation will determine the ability of researchers to decipher its role in plant-herbivore and plant-pathogen interactions.
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Mostowy R, Engelstädter J. Host–parasite coevolution induces selection for condition‐dependent sex. J Evol Biol 2012; 25:2033-2046. [DOI: 10.1111/j.1420-9101.2012.02584.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 06/04/2012] [Accepted: 06/27/2012] [Indexed: 11/27/2022]
Affiliation(s)
- R. Mostowy
- Institute for Integrative Biology ETH Zurich Zurich Switzerland
- Department of Infectious Disease Epidemiology Imperial College London London UK
| | - J. Engelstädter
- Institute for Biogeochemistry and Pollutant Dynamics ETH Zurich Zurich Switzerland
- School of Biological Sciences The University of Queensland Brisbane Qld Australia
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Zemp FJ, Sidler C, Kovalchuk I. Increase in recombination rate in Arabidopsis thaliana plants sharing gaseous environment with X-ray and UVC-irradiated plants depends on production of radicals. PLANT SIGNALING & BEHAVIOR 2012; 7:782-787. [PMID: 22751301 PMCID: PMC3583963 DOI: 10.4161/psb.20571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
X-ray and UVC are the two physical agents that damage DNA directly, with both agents capable of inducing double-strand breaks. Some of our recent work has demonstrated that local exposure to UVC results in a systemic increase in recombination frequency, suggesting that information about exposure can be passed from damaged to non-damaged tissue. Indeed, we recently showed that plants sharing the same enclosed environment with UVC-irradiated plants exhibit similar increase in homologous recombination frequency as irradiated plants. Here, we further tested whether yet another DNA-damaging agent, X-ray, is capable of increasing recombination rate (RR) in neighboring plants grown in a Petri dish. To test this, we grew plants exposed to X-ray or UVC irradiation in an enclosed environment next to non-exposed plants. We found that both X-ray and UVC-irradiated plants and neighboring plants exhibited comparable increases in the levels of strand breaks and the RR. We further showed that pre-exposure of plants to radical scavenger DMSO substantially alleviates the radiation-induced increase in RR and prevents formation of bystander signal. Our results suggest that the increase in RR in bystander plants can also be triggered by X-ray and that radicals may play some role in initiation or maintenance of this signal.
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Mandal R, Kathiria P, Psychogios N, Bouatra S, Krishnamurthy R, Wishart D, Kovalchuk I. Progeny of tobacco mosaic virus-infected Nicotiana tabacum plants exhibit trans-generational changes in metabolic profiles. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rahavi MR, Migicovsky Z, Titov V, Kovalchuk I. Transgenerational adaptation to heavy metal salts in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2011; 2:91. [PMID: 22639617 PMCID: PMC3355606 DOI: 10.3389/fpls.2011.00091] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 11/15/2011] [Indexed: 05/19/2023]
Abstract
Exposure to abiotic and biotic stress results in changes in plant physiology and triggers genomic instability. Recent reports suggest that the progeny of stressed plants also exhibit changes in genome stability, stress tolerance, and methylation. Here we analyzed whether exposure to Ni(2+), Cd(2+), and Cu(2+) salts leads to transgenerational changes in homologous recombination frequency and stress tolerance. We found that the immediate progeny of stressed plants exhibited an increased rate of recombination. However, when the progeny of stressed plants was propagated without stress, recombination reverted to normal levels. Exposure of plants to heavy metals for five consecutive generations (S1-S5) resulted in recombination frequency being maintained at a high level. Skipping stress following two to three generations of propagation with 50 mM Ni(2+) or Cd(2+) did not decrease the recombination frequency, suggesting plant acclimation to upregulated recombination. Analysis of the progeny of plants exposed to Cu(2+) and Ni(2+) indicated higher stress tolerance to the heavy metal parental plants were exposed to. Tolerance was higher in plants propagated with stress for three to five generations, which resulted in longer roots than plants propagated on heavy metals for only one to two generations. Tolerance was also more prominent upon exposure to a higher concentration of salts. The progeny of stressed plants were also more tolerant to NaCl and methyl methane sulfonate.
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Affiliation(s)
- Mohammad Reza Rahavi
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Zoë Migicovsky
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Viktor Titov
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
- *Correspondence: Igor Kovalchuk, Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4. e-mail:
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