151
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Töpfer N, Caldana C, Grimbs S, Willmitzer L, Fernie AR, Nikoloski Z. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. THE PLANT CELL 2013; 25:1197-211. [PMID: 23613196 PMCID: PMC3663262 DOI: 10.1105/tpc.112.108852] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/18/2013] [Accepted: 04/05/2013] [Indexed: 05/21/2023]
Abstract
Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.
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Affiliation(s)
- Nadine Töpfer
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory, Integrate Brazilian Center of Research in Energy and Materials, Associated Centers to the Brazilian Association for Synchrotron Light Technology, 13083-970 Campinas, Brazil
| | - Sergio Grimbs
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Lothar Willmitzer
- Genes and Small Molecules Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Address correspondence to
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152
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Popova OV, Dinh HQ, Aufsatz W, Jonak C. The RdDM pathway is required for basal heat tolerance in Arabidopsis. MOLECULAR PLANT 2013; 6:396-410. [PMID: 23376771 PMCID: PMC3603006 DOI: 10.1093/mp/sst023] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/20/2013] [Indexed: 05/19/2023]
Abstract
Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epigenetic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methylation, histone modifications, chromatin-remodeling, or siRNA-based silencing pathways. Plants deficient in NRPD2, the common second-largest subunit of RNA polymerases IV and V, and in the Rpd3-type histone deacetylase HDA6 were hypersensitive to heat exposure. Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress. The misexpression of protein-coding genes in nrpd2 mutants recovering from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription. We provide evidence that the transcriptional response to temperature stress, at least partially, relies on the integrity of the RNA-dependent DNA methylation pathway.
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Affiliation(s)
| | | | | | - Claudia Jonak
- To whom correspondence should be addressed. E-mail , tel. +43 1 790449850, fax +43 1 790449001
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153
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Grossniklaus U, Kelly WG, Ferguson-Smith AC, Pembrey M, Lindquist S. Transgenerational epigenetic inheritance: how important is it? Nat Rev Genet 2013; 14:228-35. [PMID: 23416892 PMCID: PMC4066847 DOI: 10.1038/nrg3435] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Much attention has been given to the idea of transgenerational epigenetic inheritance, but fundamental questions remain regarding how much takes place and the impact that this might have on organisms. We asked five leading researchers in this area--working on a range of model organisms and in human disease--for their views on these topics. Their responses highlight the mixture of excitement and caution that surrounds transgenerational epigenetic inheritance and the wide gulf between species in terms of our knowledge of the mechanisms that may be involved.
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Affiliation(s)
- Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
| | - William G. Kelly
- Biology Department, Emory University, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
| | - Anne C. Ferguson-Smith
- Department of Physiology, Development and Neuroscience and the Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Marcus Pembrey
- Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London WC1N 1EH, UK; Avon Longitudinal Study of Parents and Children, School of Social and Community Medicine, Oakfield House, Oakfield Grove, University of Bristol, Bristol BS8 2BN, UK.
| | - Susan Lindquist
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
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154
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Kravets AP, Sokolova DA, Vengzhen GS, Grodzinsky DM. Corn plant DNA methylation pattern changes at UV- C irradiation fractionating. CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713010052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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155
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156
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Bräutigam K, Vining KJ, Lafon-Placette C, Fossdal CG, Mirouze M, Marcos JG, Fluch S, Fraga MF, Guevara MÁ, Abarca D, Johnsen Ø, Maury S, Strauss SH, Campbell MM, Rohde A, Díaz-Sala C, Cervera MT. Epigenetic regulation of adaptive responses of forest tree species to the environment. Ecol Evol 2013; 3:399-415. [PMID: 23467802 PMCID: PMC3586649 DOI: 10.1002/ece3.461] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/19/2012] [Accepted: 11/27/2012] [Indexed: 12/25/2022] Open
Abstract
Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular "memory". Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate change.
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Affiliation(s)
- Katharina Bräutigam
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
| | - Kelly J Vining
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Clément Lafon-Placette
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Carl G Fossdal
- Department of Biology and Environment, Norwegian Forest and Landscape InstitutePO Box 115, N-1431, Aas, Norway
| | - Marie Mirouze
- Epigenetic Regulations and Seed Development, Institut de Recherche pour le Développement, UMR232 ERL5300 CNRS-IRD911 Av. Agropolis, 34394, Montpellier, France
| | - José Gutiérrez Marcos
- School of Life Sciences, University of WarwickWellesbourne, Warkwick, CV35 9EF, United Kingdom
| | - Silvia Fluch
- Platform for Integrated Clone Management (PICME), Health & Environment Department, AIT Austrian Institute of Technology GmbHKonrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Mario Fernández Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA–HUCA), University of OviedoSpain
| | - M Ángeles Guevara
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
| | - Dolores Abarca
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - Øystein Johnsen
- Department of Plant and Environmental Sciences, Norwegian University of Life SciencesPO Box 5003, N-1432, Ås, Norway
| | - Stéphane Maury
- UFR-Faculté des Sciences, UPRES EA 1207 ‘Laboratoire de Biologie des Ligneux et des Grandes Cultures’ (LBLGC), INRA, USC1328 ‘Arbres et Réponses aux Contraintes Hydrique et Environnementales’ (ARCHE), University of OrléansRue de Chartres, BP 6759, F-45067, Orléans, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State UniversityCorvallis, OR, 97331-5752, USA
| | - Malcolm M Campbell
- Centre for the Analysis of Genome Evolution and Function, Department of Cell & Systems Biology, University of TorontoToronto, ON, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, University of Toronto1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Antje Rohde
- Department Plant Growth & Development, Institute of Agriculture and Fisheries ResearchCaritasstraat 21, 9090, Melle, Belgium
| | - Carmen Díaz-Sala
- Department of Life Sciences, University of AlcaláCtra. Madrid-Barcelona Km. 33,600, 28871, Alcalá de Henares, Madrid, Spain
| | - María-Teresa Cervera
- Dpt. of Forest Ecology and Genetics, Forest Genomics and Ecophysiology group, Forest Research Centre (CIFOR). INIACrta. La Coruña km 7,5, 28040, Madrid, Spain
- Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPMMadrid, Spain
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157
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Plastics derived endocrine disruptors (BPA, DEHP and DBP) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. PLoS One 2013; 8:e55387. [PMID: 23359474 PMCID: PMC3554682 DOI: 10.1371/journal.pone.0055387] [Citation(s) in RCA: 542] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 12/28/2012] [Indexed: 12/26/2022] Open
Abstract
Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1–F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the “plastics” or “lower dose plastics” mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.
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158
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Abstract
The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects.
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Affiliation(s)
- Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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159
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A. Sokolova D, S. Vengzhen G, P. Kravets A. An Analysis of the Correlation between the Changes in Sa-tellite DNA Methylation Patterns and Plant Cell Responses to the Stress. Cell 2013. [DOI: 10.4236/cellbio.2013.23018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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160
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Aversano R, Caruso I, Aronne G, Micco VD, Scognamiglio N, Carputo D. Stochastic changes affect Solanum wild species following autopolyploidization. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:625-35. [PMID: 23307917 PMCID: PMC3542052 DOI: 10.1093/jxb/ers357] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Polyploidy is very common within angiosperms, and several studies are in progress to ascertain the effects of early polyploidization at the molecular, physiological, and phenotypic level. Extensive studies are available only in synthetic allopolyploids. By contrast, less is known about the consequences of autopolyploidization. The current study aimed to assess the occurrence and extent of genetic, epigenetic, and anatomical changes occurring after oryzaline-induced polyploidization of Solanum commersonii Dunal and Solanum bulbocastanum Dunal, two diploid (2n=2×=24) potato species widely used in breeding programmes. Microsatellite analysis showed no polymorphisms between synthetic tetraploids and diploid progenitors. By contrast, analysis of DNA methylation levels indicated that subtle alterations at CG and CHG sites were present in tetraploids of both species. However, no change occurred concurrently in all tetraploids analysed with respect to their diploid parent, revealing a stochastic trend in the changes observed. The morpho-anatomical consequences of polyploidization were studied in leaf main veins and stomata. With only a few exceptions, analyses showed no clear superiority of tetraploids in terms of leaf thickness and area, vessel number, lumen size and vessel wall thickness, stomata pore length and width, guard cell width, and stomatal density compared with their diploid progenitors. These results are consistent with the hypothesis that there are no traits systematically associated with autopolyploidy.
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Affiliation(s)
- Riccardo Aversano
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Immacolata Caruso
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Giovanna Aronne
- Department of Arboriculture, Botany and Plant Pathology, University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Veronica De Micco
- Department of Arboriculture, Botany and Plant Pathology, University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Nunzia Scognamiglio
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
| | - Domenico Carputo
- Department of Soil, Plant, Environmental and Animal Production Sciences (DiSSPAPA), University of Naples Federico II, Via Università 100, 80055 Portici (Na), Italy
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161
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Castonguay Y, Dubé MP, Cloutier J, Bertrand A, Michaud R, Laberge S. Molecular physiology and breeding at the crossroads of cold hardiness improvement. PHYSIOLOGIA PLANTARUM 2013; 147:64-74. [PMID: 22452626 DOI: 10.1111/j.1399-3054.2012.01624.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Alfalfa (Medicago sativa L.) is a major forage legume grown extensively worldwide with important agronomic and environmental attributes. Insufficient cold hardiness is a major impediment to its reliable production in northern climates. Improvement of freezing tolerance using conventional breeding approaches is slowed by the quantitative nature of inheritance and strong interactions with the environment. The development of gene-based markers would facilitate the identification of genotypes with superior stress tolerance. Successive cycles of recurrent selection were applied using an indoor screening method to develop populations with significantly higher tolerance to freezing (TF). Bulk segregant analysis of heterogeneous TF populations identified DNA variations that are progressively enriched in frequency in response to selection. Polymorphisms resulting from intragenic variations within a dehydrin gene were identified and could potentially lead to the development of robust selection tools. Our results illustrate the benefits of feedback interactions between germplasm development programs and molecular physiology for a deeper understanding of the molecular and genetic bases of cold hardiness.
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Affiliation(s)
- Yves Castonguay
- Soils and Crops Research Development Center, Agriculture and Agri-Food Canada, 2560 Hochelaga Boulevard, Sainte-Foy, Québec G1V 2J3, Canada.
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162
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Plastics derived endocrine disruptors (BPA, DEHP and DBP) induce epigenetic transgenerational inheritance of obesity, reproductive disease and sperm epimutations. PLoS One 2013. [PMID: 23359474 DOI: 10.1371/journal.pone.0055387\rpone-d-12-15587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1-F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the "plastics" or "lower dose plastics" mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, USA
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163
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Sharma A. Transgenerational epigenetic inheritance: focus on soma to germline information transfer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 113:439-46. [PMID: 23257323 DOI: 10.1016/j.pbiomolbio.2012.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 01/29/2023]
Abstract
In trangenerational epigenetic inheritance, phenotypic information not encoded in DNA sequence is transmitted across generations. In germline-dependent mode, memory of environmental exposure in parental generation is transmitted through gametes, leading to appearance of phenotypes in the unexposed future generations. The memory is considered to be encoded in epigenetic factors like DNA methylation, histone modifications and regulatory RNAs. Environmental exposure may cause epigenetic modifications in the germline either directly or indirectly through primarily affecting the soma. The latter possibility is most intriguing because it contradicts the established dogma that hereditary information flows only from germline to soma, not in reverse. As such, identification of the factor(s) mediating soma to germline information transfer in transgenerational epigenetic inheritance would be pathbreaking. Regulatory RNAs and hormone have previously been implicated or proposed to play a role in soma to germline communication in epigenetic inheritance. This review examines the recent examples of gametogenic transgenerational inheritance in plants and animals in order to assess if evidence of regulatory RNAs and hormones as mediators of information transfer is supported. Overall, direct evidence for both mobile regulatory RNAs and hormones is found to exist in plants. In animals, although involvement of mobile RNAs seems imminent, direct evidence of RNA-mediated soma to germline information transfer in transgenerational epigenetic inheritance is yet to be obtained. Direct evidence is also lacking for hormones in animals. However, detailed examination of recently reported examples of transgenerational inheritance reveals circumstantial evidence supporting a role of hormones in information transmission.
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Affiliation(s)
- Abhay Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi University Campus, Mall Road, Delhi 110007, India.
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164
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Tang X, Liu J, Huang S, Shi W, Miao M, Tang DF, Niu X, Xiao F, Liu Y. Roles of UV-damaged DNA binding protein 1 (DDB1) in epigenetically modifying multiple traits of agronomic importance in tomato. PLANT SIGNALING & BEHAVIOR 2012; 7:1529-32. [PMID: 23073016 PMCID: PMC3578885 DOI: 10.4161/psb.22249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Epigenetic regulation participates broadly in many fundamentally cellular and physiological processes. In this study, we found that DDB1, a protein originally identified as a factor involved in DNA repairing, plays important roles in regulating organ size, growth habit and photosynthesis in tomato via an epigenetic manner. We generated transgenic tomato plants overexpressing an alternatively spliced DDB1 transcript (DDB1(F) , prevalently present in tomato tissues) and found the primary transformants displayed small-fruited "cherry tomato" in companion with strikingly enhanced shoot branching and biomass, dark-green leaves with elevated chlorophyll accumulation, and increased soluble solids in fruits. Significantly, these phenotypic alterations did not segregate with the DDB1(F) transgene in subsequent generations, suggesting that the effect of DDB1(F) on multiple agronomic traits is implemented via an epigenetic manner and is inheritable over generations. We speculate that DDB1, as a core subunit in the recently identified CUL4-based E3 ligase complex, mediates the 26S proteasome-dependent degradation of a large number of proteins, some of which might be required for perpetuating epigenetic marks on chromatins.
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Affiliation(s)
- Xiaofeng Tang
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment; College of Life Science; State Key Laboratory of Hydraulics and Mountain River Engineering; Sichuan University; Chengdu, China
| | - Jikai Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment; College of Life Science; State Key Laboratory of Hydraulics and Mountain River Engineering; Sichuan University; Chengdu, China
| | - Shengxiong Huang
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei, China
| | - Wei Shi
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei, China
| | - Min Miao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment; College of Life Science; State Key Laboratory of Hydraulics and Mountain River Engineering; Sichuan University; Chengdu, China
- Department of Plant, Soil and Entomological Sciences; University of Idaho; Moscow, ID USA
| | - Dan feng Tang
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei, China
| | - Xiangli Niu
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei, China
| | - Fangming Xiao
- Department of Plant, Soil and Entomological Sciences; University of Idaho; Moscow, ID USA
| | - Yongsheng Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment; College of Life Science; State Key Laboratory of Hydraulics and Mountain River Engineering; Sichuan University; Chengdu, China
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei, China
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165
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Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK. Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers. Reprod Toxicol 2012; 34:694-707. [PMID: 23041264 PMCID: PMC3513496 DOI: 10.1016/j.reprotox.2012.09.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 01/20/2023]
Abstract
The endocrine disruptor vinclozolin has previously been shown to promote epigenetic transgenerational inheritance of adult onset disease in the rat. The current study was designed to investigate the transgenerational actions of vinclozolin on the mouse. Transient exposure of the F0 generation gestating female during gonadal sex determination promoted transgenerational adult onset disease in F3 generation male and female mice, including spermatogenic cell defects, testicular abnormalities, prostate abnormalities, kidney abnormalities and polycystic ovarian disease. Pathology analysis demonstrated 75% of the vinclozolin lineage animals developed disease with 34% having two or more different disease states. Interestingly, the vinclozolin induced transgenerational disease was observed in the outbred CD-1 strain, but not the inbred 129 mouse strain. Analysis of the F3 generation sperm epigenome identified differential DNA methylation regions that can potentially be utilized as epigenetic biomarkers for transgenerational exposure and disease.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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166
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Novy A, Flory S, Hartman JM. Evidence for rapid evolution of phenology in an invasive grass. J Evol Biol 2012. [DOI: 10.1111/jeb.12047] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Novy
- Department of Plant Biology and Pathology; Rutgers University; New Brunswick NJ USA
- Department of Landscape Architecture; Rutgers University; New Brunswick NJ USA
- United States Botanic Garden; Washington DC USA
| | - S.L. Flory
- Agronomy Department; University of Florida; Gainesville FL USA
| | - J. M. Hartman
- Department of Landscape Architecture; Rutgers University; New Brunswick NJ USA
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167
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Cominelli E, Conti L, Tonelli C, Galbiati M. Challenges and perspectives to improve crop drought and salinity tolerance. N Biotechnol 2012; 30:355-61. [PMID: 23165101 DOI: 10.1016/j.nbt.2012.11.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/05/2012] [Indexed: 11/29/2022]
Abstract
Drought and high salinity are two major abiotic stresses affecting crop productivity. Therefore, the development of crops better adapted to cope with these stresses represents a key goal to ensure global food security to an increasing world population. Although many genes involved in the response to these abiotic stresses have been extensively characterised and some stress tolerant plants developed, the success rate in producing stress-tolerant crops for field conditions has been thus far limited. In this review we discuss different factors hampering the successful transfer of beneficial genes from model species to crops, emphasizing some limitations in the phenotypic characterisation and definition of the stress tolerant plants developed so far. We also highlight some technological advances and different approaches that may help in developing cultivated stress tolerant plants.
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Affiliation(s)
- Eleonora Cominelli
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via E. Bassini 15, 20133 Milano, Italy
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168
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Skinner MK, Mohan M, Haque MM, Zhang B, Savenkova MI. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions. Genome Biol 2012; 13:R91. [PMID: 23034163 PMCID: PMC3491419 DOI: 10.1186/gb-2012-13-10-r91] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 08/23/2012] [Accepted: 10/03/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Environmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity. RESULTS Investigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes. CONCLUSIONS Combined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University,
Pullman, WA 99164-4236, USA
| | - Manikkam Mohan
- Center for Reproductive Biology, School of Biological Sciences, Washington State University,
Pullman, WA 99164-4236, USA
| | - Md M Haque
- Center for Reproductive Biology, School of Biological Sciences, Washington State University,
Pullman, WA 99164-4236, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Mount
Sinai School of Medicine, New York, NY 10029, USA
| | - Marina I Savenkova
- Center for Reproductive Biology, School of Biological Sciences, Washington State University,
Pullman, WA 99164-4236, USA
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169
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Dioxin (TCDD) induces epigenetic transgenerational inheritance of adult onset disease and sperm epimutations. PLoS One 2012; 7:e46249. [PMID: 23049995 PMCID: PMC3458876 DOI: 10.1371/journal.pone.0046249] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/30/2012] [Indexed: 01/05/2023] Open
Abstract
Environmental compounds can promote epigenetic transgenerational inheritance of adult-onset disease in subsequent generations following ancestral exposure during fetal gonadal sex determination. The current study examined the ability of dioxin (2,3,7,8-tetrachlorodibenzo[p]dioxin, TCDD) to promote epigenetic transgenerational inheritance of disease and DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to dioxin during fetal day 8 to 14 and adult-onset disease was evaluated in F1 and F3 generation rats. The incidences of total disease and multiple disease increased in F1 and F3 generations. Prostate disease, ovarian primordial follicle loss and polycystic ovary disease were increased in F1 generation dioxin lineage. Kidney disease in males, pubertal abnormalities in females, ovarian primordial follicle loss and polycystic ovary disease were increased in F3 generation dioxin lineage animals. Analysis of the F3 generation sperm epigenome identified 50 differentially DNA methylated regions (DMR) in gene promoters. These DMR provide potential epigenetic biomarkers for transgenerational disease and ancestral environmental exposures. Observations demonstrate dioxin exposure of a gestating female promotes epigenetic transgenerational inheritance of adult onset disease and sperm epimutations.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Rebecca Tracey
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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170
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Havecker ER, Wallbridge LM, Fedito P, Hardcastle TJ, Baulcombe DC. Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts. PLoS One 2012; 7:e45242. [PMID: 23028873 PMCID: PMC3447930 DOI: 10.1371/journal.pone.0045242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 08/17/2012] [Indexed: 01/26/2023] Open
Abstract
Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5′ transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.
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Affiliation(s)
- Ericka R. Havecker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Laura M. Wallbridge
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Paola Fedito
- BIOMAA, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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171
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Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK. Pesticide and insect repellent mixture (permethrin and DEET) induces epigenetic transgenerational inheritance of disease and sperm epimutations. Reprod Toxicol 2012; 34:708-19. [PMID: 22975477 DOI: 10.1016/j.reprotox.2012.08.010] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 11/16/2022]
Abstract
Environmental compounds are known to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a "pesticide mixture" (pesticide permethrin and insect repellent N,N-diethyl-meta-toluamide, DEET) promotes epigenetic transgenerational inheritance of disease and associated DNA methylation epimutations in sperm. Gestating F0 generation female rats were exposed during fetal gonadal sex determination and the incidence of disease evaluated in F1 and F3 generations. There were significant increases in the incidence of total diseases in animals from pesticide lineage F1 and F3 generation animals. Pubertal abnormalities, testis disease, and ovarian disease (primordial follicle loss and polycystic ovarian disease) were increased in F3 generation animals. Analysis of the pesticide lineage F3 generation sperm epigenome identified 363 differential DNA methylation regions (DMR) termed epimutations. Observations demonstrate that a pesticide mixture (permethrin and DEET) can promote epigenetic transgenerational inheritance of adult onset disease and potential sperm epigenetic biomarkers for ancestral environmental exposures.
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Affiliation(s)
- Mohan Manikkam
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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172
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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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173
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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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174
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Abstract
The rapid rate of current global climate change is having strong effects on many species and, at least in some cases, is driving evolution, particularly when changes in conditions alter patterns of selection. Climate change thus provides an opportunity for the study of the genetic basis of adaptation. Such studies include a variety of observational and experimental approaches, such as sampling across clines, artificial evolution experiments, and resurrection studies. These approaches can be combined with a number of techniques in genetics and genomics, including association and mapping analyses, genome scans, and transcription profiling. Recent research has revealed a number of candidate genes potentially involved in climate change adaptation and has also illustrated that genetic regulatory networks and epigenetic effects may be particularly relevant for evolution driven by climate change. Although genetic and genomic data are rapidly accumulating, we still have much to learn about the genetic architecture of climate change adaptation.
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Affiliation(s)
- Steven J Franks
- Department of Biological Sciences, Fordham University, Bronx, New York 10458, USA.
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175
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Liu J, Tang X, Gao L, Gao Y, Li Y, Huang S, Sun X, Miao M, Zeng H, Tian X, Niu X, Zheng L, Giovannoni J, Xiao F, Liu Y. A role of tomato UV-damaged DNA binding protein 1 (DDB1) in organ size control via an epigenetic manner. PLoS One 2012; 7:e42621. [PMID: 22927934 PMCID: PMC3424292 DOI: 10.1371/journal.pone.0042621] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/10/2012] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modification generally refers to phenotypic changes by a mechanism other than changes in DNA sequence and plays a significant role in developmental processes. In this study, we found that overexpression of one alternatively spliced tomato DDB1 transcript, DDB1(F) that is prevalently present in all tested tissues, resulted in reduction of organ size. Transgenic plants constitutively expressing the DDB1(F) from a strong cauliflower mosaic virus (CaMV) 35S promoter displayed moderately reduced size in vegetative organs (leaves and stems) and radically decreased size in reproductive organs (flowers, seeds and fruits), in which several genes encoding negative regulators for cell division were upregulated. Significantly, reduction of organ size conferred by overexpression of DDB1(F) transgene appears not to segregate in the subsequent generations, suggesting the phenotypic alternations are manipulated in an epigenetic manner and can be transmitted over generations. This notion was further substantiated by analysis of DNA methylation level at the SlWEE1 gene (encoding a negative regulator of cell division), revealing a correlation between less methylation in the promoter region and elevated expression level of this gene. Thus, our results suggest DDB1 plays an important role in regulation of the epigenetic state of genes involved in organogenesis, despite the underlying mechanism remains to be elucidated.
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Affiliation(s)
- Jikai Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Xiaofeng Tang
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Lanyang Gao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Yongfeng Gao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Yuxiang Li
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Shengxiong Huang
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xiaochun Sun
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Min Miao
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United State of America
| | - Hui Zeng
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xuefen Tian
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
| | - Xiangli Niu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Lei Zheng
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
| | - Jim Giovannoni
- United States Department of Agriculture-Agricultural Research Service, Robert Holly Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United State of America
| | - Fangming Xiao
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United State of America
| | - Yongsheng Liu
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, China
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, China
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176
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Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC. Experimental evolution. Trends Ecol Evol 2012; 27:547-60. [PMID: 22819306 DOI: 10.1016/j.tree.2012.06.001] [Citation(s) in RCA: 483] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/03/2012] [Accepted: 06/13/2012] [Indexed: 12/26/2022]
Abstract
Experimental evolution is the study of evolutionary processes occurring in experimental populations in response to conditions imposed by the experimenter. This research approach is increasingly used to study adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses. Long applied in vaccine development, experimental evolution also finds new applications in biotechnology. Recent technological developments provide a path towards detailed understanding of the genomic and molecular basis of experimental evolutionary change, while new findings raise new questions that can be addressed with this approach. However, experimental evolution has important limitations, and the interpretation of results is subject to caveats resulting from small population sizes, limited timescales, the simplified nature of laboratory environments, and, in some cases, the potential to misinterpret the selective forces and other processes at work.
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Affiliation(s)
- Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
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177
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Hoffmann AA, Chown SL, Clusella-Trullas S. Upper thermal limits in terrestrial ectotherms: how constrained are they? Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02036.x] [Citation(s) in RCA: 447] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ary A. Hoffmann
- Departments of Zoology and Genetics; Bio21 Institute; The University of Melbourne; 30 Flemington Road; Parkville; Victoria; 3052; Australia
| | | | - Susana Clusella-Trullas
- Department of Botany and Zoology; Centre for Invasion Biology; Stellenbosch University; Private Bag X1; Matieland; 7602; South Africa
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178
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Champagne FA. Epigenetics and developmental plasticity across species. Dev Psychobiol 2012; 55:33-41. [PMID: 22711291 DOI: 10.1002/dev.21036] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/28/2012] [Indexed: 01/12/2023]
Abstract
Plasticity is a typical feature of development and can lead to divergent phenotypes. There is increasing evidence that epigenetic mechanisms, such as DNA methylation, are present across species, are modifiable by the environment, and are involved in developmental plasticity. Thus, in the context of the concept of developmental homology, epigenetic mechanisms may serve to create a process homology between species by providing a common molecular pathway through which environmental experiences shape development, ultimately leading to phenotypic diversity. This article will highlight evidence derived from across-species investigations of epigenetics, development, and plasticity which may contribute to our understanding of the homology that exists between species and between ancestors and descendants.
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Affiliation(s)
- Frances A Champagne
- Department of Psychology, Columbia University, 1190 Amsterdam Avenue, Room 406 Schermerhorn Hall, New York, NY 10027, USA.
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179
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Topp SH, Rasmussen SK. Evaluating the potential of SHI expression as a compacting tool for ornamental plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 187:19-30. [PMID: 22404829 DOI: 10.1016/j.plantsci.2012.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 01/17/2012] [Accepted: 01/18/2012] [Indexed: 05/31/2023]
Abstract
Control of plant growth, especially elongation of stems, is important in modern plant production, and many plant species, including cereals, grasses, fruit trees and ornamentals, are regularly treated chemically to control their stature and flowering time. Chemical treatments ensure short, homogenous plants, which are more robust and easy to harvest, transport and sell. Although growth retardants are an expensive and undesirable step in plant production, it is unfortunately necessary at present. Compact growth is desirable in most ornamentals and this trait can be difficult to obtain by traditional breeding. As an alternative, biotechnology could provide plant varieties with optimized growth habits. This review is an introduction to the family of SHI transcription factors, which has recently been used to produce compact plants of very diverse species. The possible functions and regulations of the SHI proteins are discussed, and the potential of using overexpression as means to dwarf plants is assessed. In conclusion the breeding of some species, especially flowering ornamentals, could benefit from this strategy. Furthermore, detailed knowledge about the role of SHI proteins in plant growth and development could help shed more light on the interactions between plant hormone signaling pathways.
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Affiliation(s)
- Sine H Topp
- Department of Agriculture and Ecology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.
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180
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Asexual reproduction induces a rapid and permanent loss of sexual reproduction capacity in the rice fungal pathogen Magnaporthe oryzae: results of in vitro experimental evolution assays. BMC Evol Biol 2012; 12:42. [PMID: 22458778 PMCID: PMC3379926 DOI: 10.1186/1471-2148-12-42] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/29/2012] [Indexed: 12/15/2022] Open
Abstract
Background Sexual reproduction is common in eukaryotic microorganisms, with few species reproducing exclusively asexually. However, in some organisms, such as fungi, asexual reproduction alternates with episodic sexual reproduction events. Fungi are thus appropriate organisms for studies of the reasons for the selection of sexuality or clonality and of the mechanisms underlying this selection. Magnaporthe oryzae, an Ascomycete causing blast disease on rice, reproduces mostly asexually in natura. Sexual reproduction is possible in vitro and requires (i) two strains of opposite mating types including (ii) at least one female-fertile strain (i.e. a strain able to produce perithecia, the female organs in which meiosis occurs). Female-fertile strains are found only in limited areas of Asia, in which evidence for contemporary recombination has recently been obtained. We induced the forced evolution of four Chinese female-fertile strains in vitro by the weekly transfer of asexual spores (conidia) between Petri dishes. We aimed to determine whether female fertility was rapidly lost in the absence of sexual reproduction and whether this loss was controlled genetically or epigenetically. Results All the strains became female-sterile after 10 to 19 rounds of selection under asexual conditions. As no single-spore isolation was carried out, the observed decrease in the production of perithecia reflected the emergence and the invasion of female-sterile mutants. The female-sterile phenotype segregated in the offspring of crosses between female-sterile evolved strains and female-fertile wild-type strains. This segregation was maintained in the second generation in backcrosses. Female-sterile evolved strains were subjected to several stresses, but none induced the restoration of female fertility. This loss of fertility was therefore probably due to genetic rather than epigenetic mechanisms. In competition experiments, female-sterile mutants produced similar numbers of viable conidia to wild-type strains, but released them more efficiently. This advantage may account for the invasion of our populations by female-sterile mutants. Conclusions We show for the first time that, in the absence of sexual reproduction, female-sterile mutants of M. oryzae rice strains can arise and increase in abundance in asexual generations. This change in phenotype was frequent and probably caused by mutation. These results suggest that female fertility may have been lost rapidly during the dispersion of the fungus from Asia to the rest of the world.
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181
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Migicovsky Z, Kovalchuk I. Epigenetic Modifications during Angiosperm Gametogenesis. FRONTIERS IN PLANT SCIENCE 2012; 3:20. [PMID: 22645573 PMCID: PMC3355800 DOI: 10.3389/fpls.2012.00020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Accepted: 01/19/2012] [Indexed: 06/01/2023]
Abstract
Angiosperms do not contain a distinct germline, but rather develop gametes from gametophyte initials that undergo cell division. These gametes contain cells that give rise to an endosperm and the embryo. DNA methylation is decreased in the vegetative nucleus (VN) and central cell nuclei (CCN) resulting in expression of transposable elements (TEs). It is thought that the siRNAs produced in response to TE expression are able to travel to the sperm cells and egg cells (EC) from VN and CCN, respectively, in order to enforce silencing there. Demethylation during gametogenesis helps ensure that even newly integrated TEs are expressed and therefore silenced by the resulting siRNA production. A final form of epigenetic control is modification of histones, which includes accumulation of the H3 variant HTR10 in mature sperm that is then completely replaced following fertilization. In females, the histone isoforms present in the EC and CCN differ, potentially helping to differentiate the two components during gametogenesis.
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Affiliation(s)
- Zoë Migicovsky
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of LethbridgeLethbridge, AB, Canada
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182
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Krasensky J, Jonak C. Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1593-1608. [PMID: 22291134 DOI: 10.1093/jxb/err460.drought] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plants regularly face adverse growth conditions, such as drought, salinity, chilling, freezing, and high temperatures. These stresses can delay growth and development, reduce productivity, and, in extreme cases, cause plant death. Plant stress responses are dynamic and involve complex cross-talk between different regulatory levels, including adjustment of metabolism and gene expression for physiological and morphological adaptation. In this review, information about metabolic regulation in response to drought, extreme temperature, and salinity stress is summarized and the signalling events involved in mediating stress-induced metabolic changes are presented.
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Affiliation(s)
- Julia Krasensky
- GMI-Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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183
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Krasensky J, Jonak C. Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1593-608. [PMID: 22291134 PMCID: PMC4359903 DOI: 10.1093/jxb/err460] [Citation(s) in RCA: 978] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants regularly face adverse growth conditions, such as drought, salinity, chilling, freezing, and high temperatures. These stresses can delay growth and development, reduce productivity, and, in extreme cases, cause plant death. Plant stress responses are dynamic and involve complex cross-talk between different regulatory levels, including adjustment of metabolism and gene expression for physiological and morphological adaptation. In this review, information about metabolic regulation in response to drought, extreme temperature, and salinity stress is summarized and the signalling events involved in mediating stress-induced metabolic changes are presented.
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Affiliation(s)
- Julia Krasensky
- GMI–Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Claudia Jonak
- GMI–Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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184
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Elkonin LA, Tsvetova MI. Heritable Effect of Plant Water Availability Conditions on Restoration of Male Fertility in the "9E" CMS-Inducing Cytoplasm of Sorghum. FRONTIERS IN PLANT SCIENCE 2012; 3:91. [PMID: 22639674 PMCID: PMC3355589 DOI: 10.3389/fpls.2012.00091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/21/2012] [Indexed: 05/05/2023]
Abstract
Heritable changes of phenotype arising in plant ontogenesis by the influence of environmental factors belong to the most intriguing genetic phenomena. An unusual inheritance pattern was detected during examination of male fertility restoration in the CMS-inducing "9E" type cytoplasm of sorghum: Rf-genes were functional in self-pollinated progeny of F(1) hybrids yet were either not expressed or poorly expressed in backcrosses of these hybrids to CMS-lines with the same cytoplasm type. In experiments on parallel growing of the same F(1) hybrid combinations in the "dry plot" and in the "irrigated plot," it was found that high level of plant water availability during panicle and pollen developmental stages significantly increased male fertility of F(1) and test-cross hybrid populations, in which fertility-restoring genes were in heterozygote state, whereas in F(2) populations the influences of water availability conditions cause less pronounce effects. Similarly, male-sterile F(1) plants, being transferred from the "dry plot" to greenhouse, produced male-fertile panicles. In addition, male-sterile plants from F(2) families, which segregated-out as recessives, being transferred to greenhouse also produced male-fertile panicles. In the progenies of these revertants that were grown in field conditions and in the "dry plot," stable inheritance of male fertility for three cycles of self-pollination was observed, and a number of stable fertile lines in the "9E" cytoplasm were obtained. However, in test-crosses of these fertile lines to CMS-lines with the "9E" cytoplasm restoration of male fertility was not observed, except the progeny of one revertant that behaved as fertility-restorer line. These data suggest that the functional state of fertility-restoring genes for the "9E" sorghum cytoplasm is epigenetically regulated trait established by the influence of environmental factors and is transmitted to sexual generations.
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Affiliation(s)
- L. A. Elkonin
- Department of Biotechnology, Agricultural Research Institute for South-East RegionSaratov, Russia
- *Correspondence: L. A. Elkonin, Department of Biotechnology, Agricultural Research Institute for South-East Region, Tulaikova street, 7, Saratov, 410010, Russia e-mail:
| | - M. I. Tsvetova
- Department of Biotechnology, Agricultural Research Institute for South-East RegionSaratov, Russia
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185
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Herman JJ, Sultan SE. Adaptive transgenerational plasticity in plants: case studies, mechanisms, and implications for natural populations. FRONTIERS IN PLANT SCIENCE 2011; 2:102. [PMID: 22639624 PMCID: PMC3355592 DOI: 10.3389/fpls.2011.00102] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/07/2011] [Indexed: 05/18/2023]
Abstract
Plants respond to environmental conditions not only by plastic changes to their own development and physiology, but also by altering the phenotypes expressed by their offspring. This transgenerational plasticity was initially considered to entail only negative effects of stressful parental environments, such as production of smaller seeds by resource- or temperature-stressed parent plants, and was therefore viewed as environmental noise. Recent evolutionary ecology studies have shown that in some cases, these inherited environmental effects can include specific growth adjustments that are functionally adaptive to the parental conditions that induced them, which can range from contrasting states of controlled laboratory environments to the complex habitat variation encountered by natural plant populations. Preliminary findings suggest that adaptive transgenerational effects can be transmitted by means of diverse mechanisms including changes to seed provisioning and biochemistry, and epigenetic modifications such as DNA methylation that can persist across multiple generations. These non-genetically inherited adaptations can influence the ecological breadth and evolutionary dynamics of plant taxa and promote the spread of invasive plants. Interdisciplinary studies that join mechanistic and evolutionary ecology approaches will be an important source of future insights.
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186
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Michel D. Basic statistical recipes for the emergence of biochemical discernment. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:498-516. [PMID: 21839109 DOI: 10.1016/j.pbiomolbio.2011.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 01/09/2023]
Abstract
An essential step towards understanding life would be to identify the very basic mechanisms responsible for the discerning behaviour of living biochemical systems, absent from randomly reacting chemical soups. One intuitively feels that this question goes beyond the particular nature of the biological molecules and should relate to general physical principles. The pre-eminent physicist Ludwig Boltzmann early envisioned life as a struggle for entropy, in concordance with the subsequent principle of self-organization out of equilibrium. Re-examination of elementary steady state biochemical systems from a statistical perspective supports this view and shows that sigmoidal responses arising from microstates elimination, are sufficient to explain innermost characteristics of life, including its capacity to convert random molecular interactions into accurate biological reactions. A primary operating strategy to achieve this goal is the introduction of time-irreversible transitions in molecular state conversion cycles by injection of free energy, which confers decisional capacity to single macromolecules. Selected examples from various fields of molecular biology such as enzymology and gene expression, are provided to show that these non-equilibrium steady state mechanisms remain important in contemporary biochemical systems. But in addition, information archiving allowed the emergence of the time-reversible counterparts of these mechanisms, mediated by evolutionary pre-organized macromolecular complexes capable of generating discernment in a non-dissipative manner.
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Affiliation(s)
- Denis Michel
- Université de Rennes1, Molecular and Cellular Interactions UMR6026, Irset. IFR140GFAS, Bat. 13, Campus de Beaulieu, 35042 Rennes Cedex, France.
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187
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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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