1
|
Song S, Wang Y, Wang J, Liu Y, Zhang X, Yang A, Li F. Low H3K27me3 deposition at CYP82E4 determines the nicotinic conversion rate in Nicotiana tabacum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108234. [PMID: 38056040 DOI: 10.1016/j.plaphy.2023.108234] [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: 06/12/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
Nicotine conversion is the process by which nornicotine is synthesized from nicotine. The capacity of a plant to carry out this process is represented by the nicotine conversion rate (NCR), which is defined as the percentage of nornicotine content out of the total nicotine + nornicotine content. Nicotine conversion in tobacco is mediated by CYP82E4. Although there are cultivar-specific differences in NCR, these do not correspond to differences in the CYP82E4 promoter or gene body sequences, and little is known about the underlying regulatory mechanism. Here, we found that histone H3 Lysine 27 trimethylation (H3K27me3) was involved in CYP82E4 expression, functioning as a transcriptional repressor. Compared to a high-NCR near-isogenic line, a low-NCR cultivar showed increased levels of the repressive histone modification markers H3K27me3 and H3K9me3 at CYP82E4. Comparison of histone markers between several cultivars with varying NCRs showed that H3K27me3 and H3K9me3 levels were significantly associated with cultivar-specific differences in NCR. Treatment with the H3K27me3 demethylase inhibitor GSK-J4 increased total H3K27me3 levels and enriched H3K27me3 at the CYP82E4 locus; the increased levels of H3K27me3 further inhibited CYP82E4 expression. Knocking out E(z), an indispensable gene for H3K27me3 formation, decreased H3K27me3 levels at CYP82E4, leading to a more than three-fold increase in CYP82E4 expression. Changes in CYP82E4 expression during leaf senescence and chilling stress were also strongly correlated with H3K27me3 levels. These findings reveal a strong correlation between CYP82E4 expression and histone modifications, and demonstrate an instance of histone-mediated alkaloid regulation for the first time.
Collapse
Affiliation(s)
- Shiyang Song
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yaqi Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Jin Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Yanfang Liu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Xingzi Zhang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China; Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Aiguo Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Fengxia Li
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| |
Collapse
|
2
|
Wang Z, Zhang Y, Kang Z, Mao H. Improvement of wheat drought tolerance through editing of TaATX4 by CRISPR/Cas9. J Genet Genomics 2023; 50:913-916. [PMID: 37820936 DOI: 10.1016/j.jgg.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
3
|
Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
Collapse
|
4
|
Katsidi EC, Avramidou EV, Ganopoulos I, Barbas E, Doulis A, Triantafyllou A, Aravanopoulos FA. Genetics and epigenetics of Pinus nigra populations with differential exposure to air pollution. FRONTIERS IN PLANT SCIENCE 2023; 14:1139331. [PMID: 37089661 PMCID: PMC10117940 DOI: 10.3389/fpls.2023.1139331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Forest species in the course of their evolution have experienced several environmental challenges, which since historic times include anthropogenic pollution. The effects of pollution on the genetic and epigenetic diversity in black pine (Pinus nigra) forests were investigated in the Amyntaio - Ptolemais - Kozani Basin, which has been for decades the largest lignite mining and burning center of Greece, with a total installed generating capacity of about 4.5 GW, operating for more than 70 years and resulting in large amounts of primary air pollutant emissions, mainly SO2, NOx and PM10. P. nigra, a biomarker for air pollution and a keystone species of affected natural ecosystems, was examined in terms of phenology (cone and seed parameters), genetics (283 AFLP loci) and epigenetics (606 MSAP epiloci), using two populations (exposed to pollution and control) of the current (mature trees) and future (embryos) stand. It was found that cone, seed, as well as genetic diversity parameters, did not show statistically significant differences between the exposed population and the control. Nevertheless, statistically significant differences were detected at the population epigenetic level. Moreover, there was a further differentiation regarding the intergenerational comparison: while the epigenetic diversity does not substantially change in the two generations assessed in the control population, epigenetic diversity is significantly higher in the embryo population compared to the parental stand in the exposed population. This study sheds a light to genome dynamics in a forest tree population exposed to long term atmospheric pollution burden and stresses the importance of assessing both genetics and epigenetics in biomonitoring applications.
Collapse
Affiliation(s)
- Elissavet Ch. Katsidi
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelos Barbas
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Doulis
- Laboratory of Plant Biotechnology – Genomic Resources, Hellenic Agricultural Organization DEMETER, Institute of Viticulture, Floriculture and Vegetable Crops, Heraklion, Greece
| | - Athanasios Triantafyllou
- Laboratory of Atmospheric Pollution and Environmental Physics (LALEP), Faculty of Engineering, University of Western Macedonia, Kozani, Greece
| | - Filippos A. Aravanopoulos
- Laboratory of Forest Genetics & Tree Breeding, Faculty of Agriculture, Forestry & Environmental Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Filippos A. Aravanopoulos,
| |
Collapse
|
5
|
Meta-Analysis Reveals Challenges and Gaps for Genome-to-Phenome Research Underpinning Plant Drought Response. Int J Mol Sci 2022; 23:ijms232012297. [PMID: 36293161 PMCID: PMC9602940 DOI: 10.3390/ijms232012297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 01/24/2023] Open
Abstract
Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways.
Collapse
|
6
|
Sun M, Yang Z, Liu L, Duan L. DNA Methylation in Plant Responses and Adaption to Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23136910. [PMID: 35805917 PMCID: PMC9266845 DOI: 10.3390/ijms23136910] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.
Collapse
Affiliation(s)
| | | | - Li Liu
- Correspondence: (L.L.); (L.D.)
| | | |
Collapse
|
7
|
de Tomás C, Bardil A, Castanera R, Casacuberta JM, Vicient CM. Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond. HORTICULTURE RESEARCH 2022; 9:uhac127. [PMID: 35928404 PMCID: PMC9343919 DOI: 10.1093/hr/uhac127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the "genomic shock" expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a "genomic shock" with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.
Collapse
Affiliation(s)
- Carlos de Tomás
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona 08193, Spain
| | - Amélie Bardil
- Institut écologie et environnement (INEE), CNRS, Montpelier, France
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona 08193, Spain
| | | | | |
Collapse
|
8
|
Sun Y, Züst T, Silvestro D, Erb M, Bossdorf O, Mateo P, Robert C, Müller-Schärer H. Climate warming can reduce biocontrol efficacy and promote plant invasion due to both genetic and transient metabolomic changes. Ecol Lett 2022; 25:1387-1400. [PMID: 35384215 PMCID: PMC9324167 DOI: 10.1111/ele.14000] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/16/2021] [Accepted: 02/22/2022] [Indexed: 01/25/2023]
Abstract
Climate change may affect plant-herbivore interactions and their associated ecosystem functions. In an experimental evolution approach, we subjected replicated populations of the invasive Ambrosia artemisiifolia to a combination of simulated warming and herbivory by a potential biocontrol beetle. We tracked genomic and metabolomic changes across generations in field populations and assessed plant offspring phenotypes in a common environment. Using an integrated Bayesian model, we show that increased offspring biomass in response to warming arose through changes in the genetic composition of populations. In contrast, increased resistance to herbivory arose through a shift in plant metabolomic profiles without genetic changes, most likely by transgenerational induction of defences. Importantly, while increased resistance was costly at ambient temperatures, warming removed this constraint and favoured both vigorous and better defended plants under biocontrol. Climate warming may thus decrease biocontrol efficiency and promote Ambrosia invasion, with potentially serious economic and health consequences.
Collapse
Affiliation(s)
- Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.,Department of Biology/Ecology & Evolution, University of Fribourg, Fribourg, Switzerland
| | - Tobias Züst
- Institute of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Daniele Silvestro
- Department of Biology/Ecology & Evolution, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland.,Department of Biological and Environmental Sciences and Global Gothenburg Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution & Ecology, University of Tübingen, Tübingen, Germany
| | - Pierre Mateo
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | - Heinz Müller-Schärer
- Department of Biology/Ecology & Evolution, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
9
|
Yadav NS, Titov V, Ayemere I, Byeon B, Ilnytskyy Y, Kovalchuk I. Multigenerational Exposure to Heat Stress Induces Phenotypic Resilience, and Genetic and Epigenetic Variations in Arabidopsis thaliana Offspring. FRONTIERS IN PLANT SCIENCE 2022; 13:728167. [PMID: 35419019 PMCID: PMC8996174 DOI: 10.3389/fpls.2022.728167] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Plants are sedentary organisms that constantly sense changes in their environment and react to various environmental cues. On a short-time scale, plants respond through alterations in their physiology, and on a long-time scale, plants alter their development and pass on the memory of stress to the progeny. The latter is controlled genetically and epigenetically and allows the progeny to be primed for future stress encounters, thus increasing the likelihood of survival. The current study intended to explore the effects of multigenerational heat stress in Arabidopsis thaliana. Twenty-five generations of Arabidopsis thaliana were propagated in the presence of heat stress. The multigenerational stressed lineage F25H exhibited a higher tolerance to heat stress and elevated frequency of homologous recombination, as compared to the parallel control progeny F25C. A comparison of genomic sequences revealed that the F25H lineage had a three-fold higher number of mutations [single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)] as compared control lineages, suggesting that heat stress induced genetic variations in the heat-stressed progeny. The F25H stressed progeny showed a 7-fold higher number of non-synonymous mutations than the F25C line. Methylome analysis revealed that the F25H stressed progeny showed a lower global methylation level in the CHH context than the control progeny. The F25H and F25C lineages were different from the parental control lineage F2C by 66,491 and 80,464 differentially methylated positions (DMPs), respectively. F25H stressed progeny displayed higher frequency of methylation changes in the gene body and lower in the body of transposable elements (TEs). Gene Ontology analysis revealed that CG-DMRs were enriched in processes such as response to abiotic and biotic stimulus, cell organizations and biogenesis, and DNA or RNA metabolism. Hierarchical clustering of these epimutations separated the heat stressed and control parental progenies into distinct groups which revealed the non-random nature of epimutations. We observed an overall higher number of epigenetic variations than genetic variations in all comparison groups, indicating that epigenetic variations are more prevalent than genetic variations. The largest difference in epigenetic and genetic variations was observed between control plants comparison (F25C vs. F2C), which clearly indicated that the spontaneous nature of epigenetic variations and heat-inducible nature of genetic variations. Overall, our study showed that progenies derived from multigenerational heat stress displayed a notable adaption in context of phenotypic, genotypic and epigenotypic resilience.
Collapse
|
10
|
Olivares-Castro G, Cáceres-Jensen L, Guerrero-Bosagna C, Villagra C. Insect Epigenetic Mechanisms Facing Anthropogenic-Derived Contamination, an Overview. INSECTS 2021; 12:780. [PMID: 34564220 PMCID: PMC8468710 DOI: 10.3390/insects12090780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/14/2022]
Abstract
Currently, the human species has been recognized as the primary species responsible for Earth's biodiversity decline. Contamination by different chemical compounds, such as pesticides, is among the main causes of population decreases and species extinction. Insects are key for ecosystem maintenance; unfortunately, their populations are being drastically affected by human-derived disturbances. Pesticides, applied in agricultural and urban environments, are capable of polluting soil and water sources, reaching non-target organisms (native and introduced). Pesticides alter insect's development, physiology, and inheritance. Recently, a link between pesticide effects on insects and their epigenetic molecular mechanisms (EMMs) has been demonstrated. EMMs are capable of regulating gene expression without modifying genetic sequences, resulting in the expression of different stress responses as well as compensatory mechanisms. In this work, we review the main anthropogenic contaminants capable of affecting insect biology and of triggering EMMs. EMMs are involved in the development of several diseases in native insects affected by pesticides (e.g., anomalous teratogenic reactions). Additionally, EMMs also may allow for the survival of some species (mainly pests) under contamination-derived habitats; this may lead to biodiversity decline and further biotic homogenization. We illustrate these patterns by reviewing the effect of neonicotinoid insecticides, insect EMMs, and their ecological consequences.
Collapse
Affiliation(s)
- Gabriela Olivares-Castro
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| | - Lizethly Cáceres-Jensen
- Laboratorio de Físicoquímica Analítica, Departamento de Química, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Santiago 7760197, Chile;
| | - Carlos Guerrero-Bosagna
- Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden;
- Environmental Toxicology Program, Department of Integrative Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Cristian Villagra
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Avenida José Pedro Alessandri 774, Santiago 7760197, Chile;
| |
Collapse
|
11
|
Li WF, Ning GX, Zuo CW, Chu MY, Yang SJ, Ma ZH, Zhou Q, Mao J, Chen BH. MYB_SH[AL]QKY[RF] transcription factors MdLUX and MdPCL-like promote anthocyanin accumulation through DNA hypomethylation and MdF3H activation in apple. TREE PHYSIOLOGY 2021; 41:836-848. [PMID: 33171489 DOI: 10.1093/treephys/tpaa156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/20/2020] [Accepted: 11/08/2020] [Indexed: 05/14/2023]
Abstract
Heritable DNA methylation is a highly conserved epigenetic mark that is important for many biological processes. In a previous transcriptomic study on the fruit skin pigmentation of apple (Malus domestica Borkh.) cv. 'Red Delicious' (G0) and its four continuous-generation bud sport mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee spur' (G4), we identified MYB transcription factors (TFs) MdLUX and MdPCL-like involved in regulating anthocyanin synthesis. However, how these TFs ultimately determine the fruit skin color traits remains elusive. Here, bioinformatics analysis revealed that MdLUX and MdPCL-like contained a well-conserved motif SH[AL]QKY[RF] in their C-terminal region and were located in the nucleus of onion epidermal cells. Overexpression of MdLUX and MdPCL-like in 'Golden Delicious' fruits, 'Gala' calli and Arabidopsis thaliana promoted the accumulation of anthocyanin, whereas MdLUX and MdPCL-like suppression inhibited anthocyanin accumulation in 'Red Fuji' apple fruit skin. Yeast one-hybrid assays revealed that MdLUX and MdPCL-like may bind to the promoter region of the anthocyanin biosynthesis gene MdF3H. Dual-luciferase assays indicated that MdLUX and MdPCL-like activated MdF3H. The whole-genome DNA methylation study revealed that the methylation levels of the mCG context at the upstream (i.e., promoter region) of MdLUX and MdPCL-like were inversely correlated with their mRNA levels and anthocyanin accumulation. Hence, the data suggest that MYB_SH[AL]QKY[RF] TFs MdLUX and MdPCL-like promote anthocyanin biosynthesis in apple fruit skins through the DNA hypomethylation of their promoter regions and the activation of the structural flavonoid gene MdF3H.
Collapse
Affiliation(s)
- Wen-Fang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Gai-Xing Ning
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Cun-Wu Zuo
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Ming-Yu Chu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Shi-Jin Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zong-Huan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Qi Zhou
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Bai-Hong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
Collapse
|
14
|
Liu S, de Jonge J, Trejo‐Arellano MS, Santos‐González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. THE NEW PHYTOLOGIST 2021; 229:2238-2250. [PMID: 33091182 PMCID: PMC7894476 DOI: 10.1111/nph.17018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 05/03/2023]
Abstract
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
Collapse
Affiliation(s)
- Shujing Liu
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jennifer de Jonge
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Minerva S. Trejo‐Arellano
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Juan Santos‐González
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Claudia Köhler
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Lars Hennig
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| |
Collapse
|
15
|
Gutzat R, Mittelsten Scheid O. Preparing Chromatin and RNA from Rare Cell Types with Fluorescence-Activated Nuclear Sorting (FANS). Methods Mol Biol 2020; 2093:95-105. [PMID: 32088891 DOI: 10.1007/978-1-0716-0179-2_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The application of fluorescent tags to generate cell type-specific translational and transcriptional reporter lines is routine in plants, but separation of different cell types for downstream analyses is hampered by the presence of cell walls and tight connections between cells. Enzymatic removal of cell walls induces a wound response, dedifferentiation, or reprogramming of the resulting protoplasts. Their osmotic and mechanical instability and their large size range are challenging for FACS, a flow -sorting procedure based on differential expression of fluorescent tags. In contrast, plant nuclei are relatively robust and easy to isolate. Here, we describe a protocol for fluorescence-activated nuclear sorting (FANS) that allows efficient purification of very few fluorescence-tagged nuclei from a large background of non-labeled tissue. Purified nuclei are suitable for genome, epigenome, transcriptome, or proteome analyses. We describe in detail how to analyze nuclear RNA and DNA methylation from sorted nuclei representing the limited number of stem cells in the shoot apical meristem of Arabidopsis.
Collapse
Affiliation(s)
- Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| |
Collapse
|
16
|
Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses. Int J Mol Sci 2020; 21:ijms21207457. [PMID: 33050358 PMCID: PMC7589735 DOI: 10.3390/ijms21207457] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 01/17/2023] Open
Abstract
Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.
Collapse
|
17
|
Abstract
RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best characterized within angiosperms (flowering plants), and particularly within the model plant Arabidopsis thaliana. However, conserved RdDM pathway components and associated small RNAs (sRNAs) have also been found in other groups of plants, such as gymnosperms and ferns. The RdDM pathway closely resembles other sRNA pathways, particularly the highly conserved RNAi pathway found in fungi, plants, and animals. Both the RdDM and RNAi pathways produce sRNAs and involve conserved Argonaute, Dicer and RNA-dependent RNA polymerase proteins. RdDM has been implicated in a number of regulatory processes in plants. The DNA methylation added by RdDM is generally associated with transcriptional repression of the genetic sequences targeted by the pathway. Since DNA methylation patterns in plants are heritable, these changes can often be stably transmitted to progeny. As a result, one prominent role of RdDM is the stable, transgenerational suppression of transposable element (TE) activity. RdDM has also been linked to pathogen defense, abiotic stress responses, and the regulation of several key developmental transitions. Although the RdDM pathway has a number of important functions, RdDM-defective mutants in Arabidopsis thaliana are viable and can reproduce, which has enabled detailed genetic studies of the pathway. However, RdDM mutants can have a range of defects in different plant species, including lethality, altered reproductive phenotypes, TE upregulation and genome instability, and increased pathogen sensitivity. Overall, RdDM is an important pathway in plants that regulates a number of processes by establishing and reinforcing specific DNA methylation patterns, which can lead to transgenerational epigenetic effects on gene expression and phenotype.
Collapse
|
18
|
Wang L, Leister D, Kleine T. Chloroplast development and genomes uncoupled signaling are independent of the RNA-directed DNA methylation pathway. Sci Rep 2020; 10:15412. [PMID: 32963291 PMCID: PMC7508864 DOI: 10.1038/s41598-020-71907-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/21/2020] [Indexed: 01/18/2023] Open
Abstract
The Arabidopsis genome is methylated in CG and non-CG (CHG, and CHH in which H stands for A, T, or C) sequence contexts. DNA methylation has been suggested to be critical for seed development, and CHH methylation patterns change during stratification and germination. In plants, CHH methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. To test for an involvement of the RdDM pathway in chloroplast development, we analyzed seedling greening and the maximum quantum yield of photosystem II (Fv/Fm) in Arabidopsis thaliana seedlings perturbed in components of that pathway. Neither seedling greening nor Fv/Fm in seedlings and adult plants were affected in this comprehensive set of mutants, indicating that alterations in the RdDM pathway do not affect chloroplast development. Application of inhibitors like lincomycin or norflurazon inhibits greening of seedlings and represses the expression of photosynthesis-related genes including LIGHT HARVESTING CHLOROPHYLL A/B BINDING PROTEIN1.2 (LHCB1.2) in the nucleus. Our results indicate that the LHCB1.2 promoter is poorly methylated under both control conditions and after inhibitor treatment. Therefore no correlation between LHCB1.2 mRNA transcription and methylation changes of the LHCB1.2 promoter could be established. Moreover, we conclude that perturbations in the RdDM pathway do not interfere with gun signaling.
Collapse
Affiliation(s)
- Liangsheng Wang
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| |
Collapse
|
19
|
Gahlaut V, Samtani H, Khurana P. Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum). Genomics 2020; 112:4796-4807. [PMID: 32890700 DOI: 10.1016/j.ygeno.2020.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023]
Abstract
DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.
Collapse
Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| |
Collapse
|
20
|
Caffeine effects on systemic metabolism, oxidative-inflammatory pathways, and exercise performance. Nutr Res 2020; 80:1-17. [DOI: 10.1016/j.nutres.2020.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/11/2020] [Accepted: 05/09/2020] [Indexed: 01/06/2023]
|
21
|
Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
Collapse
Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| |
Collapse
|
22
|
Omony J, Nussbaumer T, Gutzat R. DNA methylation analysis in plants: review of computational tools and future perspectives. Brief Bioinform 2020; 21:906-918. [PMID: 31220217 DOI: 10.1093/bib/bbz039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/28/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.
Collapse
Affiliation(s)
- Jimmy Omony
- Plant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Nussbaumer
- Institute of Network Biology, Department of Environmental Science, Helmholtz Center Munich, Neuherberg, Germany.,Institute of Environmental Medicine, UNIKA-T, Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Augsburg, Germany; CK CARE Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| |
Collapse
|
23
|
Eriksson MC, Szukala A, Tian B, Paun O. Current research frontiers in plant epigenetics: an introduction to a Virtual Issue. THE NEW PHYTOLOGIST 2020; 226:285-288. [PMID: 32180259 PMCID: PMC7154677 DOI: 10.1111/nph.16493] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
http://www.newphytologist.com/virtualissues
Collapse
Affiliation(s)
- Mimmi C. Eriksson
- Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Vienna Graduate School of Population GeneticsVeterinärplatz 1A‐1210ViennaAustria
| | - Aglaia Szukala
- Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Vienna Graduate School of Population GeneticsVeterinärplatz 1A‐1210ViennaAustria
| | - Bin Tian
- Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Southwest Forestry UniversityKunming650224China
| | - Ovidiu Paun
- Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| |
Collapse
|
24
|
Lamelas L, Valledor L, Escandón M, Pinto G, Cañal MJ, Meijón M. Integrative analysis of the nuclear proteome in Pinus radiata reveals thermopriming coupled to epigenetic regulation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2040-2057. [PMID: 31781741 PMCID: PMC7094079 DOI: 10.1093/jxb/erz524] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
Despite it being an important issue in the context of climate change, for most plant species it is not currently known how abiotic stresses affect nuclear proteomes and mediate memory effects. This study examines how Pinus radiata nuclei respond, adapt, 'remember', and 'learn' from heat stress. Seedlings were heat-stressed at 45 °C for 10 d and then allowed to recover. Nuclear proteins were isolated and quantified by nLC-MS/MS, the dynamics of tissue DNA methylation were examined, and the potential acquired memory was analysed in recovered plants. In an additional experiment, the expression of key gene genes was also quantified. Specific nuclear heat-responsive proteins were identified, and their biological roles were evaluated using a systems biology approach. In addition to heat-shock proteins, several clusters involved in regulation processes were discovered, such as epigenomic-driven gene regulation, some transcription factors, and a variety of RNA-associated functions. Nuclei exhibited differential proteome profiles across the phases of the experiment, with histone H2A and methyl cycle enzymes in particular being accumulated in the recovery step. A thermopriming effect was possibly linked to H2A abundance and over-accumulation of spliceosome elements in recovered P. radiata plants. The results suggest that epigenetic mechanisms play a key role in heat-stress tolerance and priming mechanisms.
Collapse
Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Escandón
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - Gloria Pinto
- Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Oviedo, Asturias, Spain
| |
Collapse
|
25
|
Wang M, Yuan J, Qin L, Shi W, Xia G, Liu S. TaCYP81D5, one member in a wheat cytochrome P450 gene cluster, confers salinity tolerance via reactive oxygen species scavenging. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:791-804. [PMID: 31472082 PMCID: PMC7004906 DOI: 10.1111/pbi.13247] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 05/03/2023]
Abstract
As one of the largest gene families in plants, the cytochrome P450 monooxygenase genes (CYPs) are involved in diverse biological processes including biotic and abiotic stress response. Moreover, P450 genes are prone to expanding due to gene tandem duplication during evolution, resulting in generations of novel alleles with the neo-function or enhanced function. Here, the bread wheat (Triticum aestivum) gene TaCYP81D5 was found to lie within a cluster of five tandemly arranged CYP81D genes, although only a single such gene (BdCYP81D1) was present in the equivalent genomic region of the wheat relative Brachypodium distachyon. The imposition of salinity stress could up-regulate TaCYP81D5, but the effect was abolished in plants treated with an inhibitor of reactive oxygen species synthesis. In SR3, a wheat cultivar with an elevated ROS content, the higher expression and the rapider response to salinity of TaCYP81D5 were related to the chromatin modification. Constitutively expressing TaCYP81D5 enhanced the salinity tolerance both at seedling and reproductive stages of wheat via accelerating ROS scavenging. Moreover, an important component of ROS signal transduction, Zat12, was proven crucial in this process. Though knockout of solely TaCYP81D5 showed no effect on salinity tolerance, knockdown of BdCYP81D1 or all TaCYP81D members in the cluster caused the sensitivity to salt stress. Our results provide the direct evidence that TaCYP81D5 confers salinity tolerance in bread wheat and this gene is prospective for crop improvement.
Collapse
Affiliation(s)
- Meng Wang
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjingChina
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Jiarui Yuan
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Lumin Qin
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil ScienceChinese Academy of SciencesNanjingChina
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Shuwei Liu
- Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| |
Collapse
|
26
|
Konate M, Wilkinson MJ, Taylor J, Scott ES, Berger B, Rodriguez Lopez CM. Greenhouse Spatial Effects Detected in the Barley ( Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation. FRONTIERS IN PLANT SCIENCE 2020; 11:553907. [PMID: 33013971 PMCID: PMC7511590 DOI: 10.3389/fpls.2020.553907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/24/2020] [Indexed: 05/10/2023]
Abstract
Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others have been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome, and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-sensitive amplified polymorphism (MSAP) and phenotypic analyses of nine diverse barley varieties were grown in a randomized plot design, under two salt treatments (0 and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.
Collapse
Affiliation(s)
- Moumouni Konate
- Institut de l'Environnement et de Recherche Agricole (INERA), DRREA-Ouest, Bobo Dioulasso, Burkina Faso
| | - Michael J. Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth, United Kingdom
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
| | - Julian Taylor
- Biometry Hub, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Eileen S. Scott
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Carlos Marcelino Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
- *Correspondence: Carlos Marcelino Rodriguez Lopez, ; Michael J. Wilkinson,
| |
Collapse
|
27
|
Guo X, Xie Q, Li B, Su H. Molecular characterization and transcription analysis of DNA methyltransferase genes in tomato (Solanum lycopersicum). Genet Mol Biol 2019; 43:e20180295. [PMID: 31429858 PMCID: PMC7197986 DOI: 10.1590/1678-4685-gmb-2018-0295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/08/2019] [Indexed: 11/22/2022] Open
Abstract
DNA methylation plays an important role in plant growth and development, gene expression regulation, and maintenance of genome stability. However, only little information regarding stress-related DNA methyltransferases (MTases) genes is available in tomato. Here, we report the analysis of nine tomato MTases, which were categorized into four known subfamilies. Structural analysis suggested their DNA methylase domains are highly conserved, whereas the N-terminals are divergent. Tissue-specific analysis of these MTase genes revealed that SlCMT2, SlCMT3, and SlDRM5 were expressed higher in young leaves, while SlMET1, SlCMT4, SlDRM7, and SlDRM8 were highly expressed in immature green fruit, and their expression declined continuously with further fruit development. In contrast, SlMETL was highly expressed in ripening fruit and displayed an up-regulated tendency during fruit development. In addition, the expression of SlMET1 in the ripening of mutant rin and Nr tomatoes is significantly higher compared to wild-type tomato, suggesting that SlMET1 was negatively regulated by the ethylene signal and ripening regulator MADS-RIN. Furthermore, expression analysis under abiotic stresses revealed that these MTase genes were stress-responsive and may function diversely in different stress conditions. Overall, our results provide valuable information for exploring the regulation of tomato fruit ripening and response to abiotic stress through DNA methylation.
Collapse
Affiliation(s)
- Xuhu Guo
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Qian Xie
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Baoyuan Li
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Huanzhen Su
- Shanxi Datong University, School of Life Sciences, Datong, China
| |
Collapse
|
28
|
Huang S, Zhang A, Jin JB, Zhao B, Wang TJ, Wu Y, Wang S, Liu Y, Wang J, Guo P, Ahmad R, Liu B, Xu ZY. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. THE NEW PHYTOLOGIST 2019; 223:1372-1387. [PMID: 31038749 DOI: 10.1111/nph.15874] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Under dehydration in plants, antagonistic activities of histone 3 lysine 4 (H3K4) methyltransferase and histone demethylase maintain a dynamic and homeostatic state of gene expression by orientating transcriptional reprogramming toward growth or stress tolerance. However, the histone demethylase that specifically controls histone methylation homeostasis under dehydration stress remains unknown. Here, we document that a histone demethylase, JMJ17, belonging to the KDM5/JARID1 family, plays crucial roles in response to dehydration stress and abscisic acid (ABA) in Arabidopsis thaliana. jmj17 loss-of-function mutants displayed dehydration stress tolerance and ABA hypersensitivity in terms of stomatal closure. JMJ17 specifically demethylated H3K4me1/2/3 via conserved iron-binding amino acids in vitro and in vivo. Moreover, H3K4 demethylase activity of JMJ17 was required for dehydration stress response. Systematic combination of genome-wide chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses revealed that a loss-of-function mutation in JMJ17 caused an ectopic increase in genome-wide H3K4me3 levels and activated a plethora of dehydration stress-responsive genes. Importantly, JMJ17 bound directly to the chromatin of OPEN STOMATA 1 (OST1) and demethylated H3K4me3 for the regulation of OST1 mRNA abundance, thereby modulating the dehydration stress response. Our results demonstrate a new function of a histone demethylase under dehydration stress in plants.
Collapse
Affiliation(s)
- Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jing Bo Jin
- Key Laboratory of Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Bo Zhao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yifan Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rafiq Ahmad
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
29
|
Testillano PS. Microspore embryogenesis: targeting the determinant factors of stress-induced cell reprogramming for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2965-2978. [PMID: 30753698 DOI: 10.1093/jxb/ery464] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/17/2018] [Indexed: 05/17/2023]
Abstract
Under stress, isolated microspores are reprogrammed in vitro towards embryogenesis, producing doubled haploid plants that are useful biotechnological tools in plant breeding as a source of new genetic variability, fixed in homozygous plants in only one generation. Stress-induced cell death and low rates of cell reprogramming are major factors that reduce yield. Knowledge gained in recent years has revealed that initiation and progression of microspore embryogenesis involve a complex network of factors, whose roles are not yet well understood. Here, I review recent findings on the determinant factors underlying stress-induced microspore embryogenesis, focusing on the role of autophagy, cell death, auxin, chromatin modifications, and the cell wall. Autophagy and cell death proteases are crucial players in the response to stress, while cell reprogramming and acquisition of totipotency are regulated by hormonal and epigenetic mechanisms. Auxin biosynthesis, transport, and action are required for microspore embryogenesis. Initial stages involve DNA hypomethylation, H3K9 demethylation, and H3/H4 acetylation. Cell wall remodelling, with pectin de-methylesterification and arabinogalactan protein expression, is necessary for embryo development. Recent reports show that treatments with small modulators of autophagy, proteases, and epigenetic marks reduce cell death and enhance embryogenesis initiation in several crops, opening up new possibilities for improving in vitro embryo production in breeding programmes.
Collapse
Affiliation(s)
- Pilar S Testillano
- Pollen Biotechnology of Crop Plants group, Biological Research Center, CIB-CSIC, Ramiro de Maeztu, Madrid, Spain
| |
Collapse
|
30
|
Moshynets OV, Babenko LM, Rogalsky SP, Iungin OS, Foster J, Kosakivska IV, Potters G, Spiers AJ. Priming winter wheat seeds with the bacterial quorum sensing signal N-hexanoyl-L-homoserine lactone (C6-HSL) shows potential to improve plant growth and seed yield. PLoS One 2019; 14:e0209460. [PMID: 30802259 PMCID: PMC6388923 DOI: 10.1371/journal.pone.0209460] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 01/07/2023] Open
Abstract
Several model plants are known to respond to bacterial quorum sensing molecules with altered root growth and gene expression patterns and induced resistance to plant pathogens. These compounds may represent novel elicitors that could be applied as seed primers to enhance cereal crop resistance to pathogens and abiotic stress and to improve yields. We investigated whether the acyl-homoserine lactone N-hexanoyl-L-homoserine lactone (C6-HSL) impacted winter wheat (Triticum aestivum L.) seed germination, plant development and productivity, using two Ukrainian varieties, Volodarka and Yatran 60, in both in vitro experiments and field trials. In vitro germination experiments indicated that C6-HSL seed priming had a small but significant positive impact on germination levels (1.2x increase, p < 0.0001), coleoptile and radicle development (1.4x increase, p < 0.0001). Field trials over two growing seasons (2015–16 and 2016–17) also demonstrated significant improvements in biomass at the tillering stage (1.4x increase, p < 0.0001), and crop structure and productivity at maturity including grain yield (1.4–1.5x increase, p < 0.0007) and quality (1.3x increase in good grain, p < 0.0001). In some cases variety effects were observed (p ≤ 0.05) suggesting that the effect of C6-HSL seed priming might depend on plant genetics, and some benefits of priming were also evident in F1 plants grown from seeds collected the previous season (p ≤ 0.05). These field-scale findings suggest that bacterial acyl-homoserine lactones such as C6-HSL could be used to improve cereal crop growth and yield and reduce reliance on fungicides and fertilisers to combat pathogens and stress.
Collapse
Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
- * E-mail: (OM); (AS)
| | - Lidia M. Babenko
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Sergiy P. Rogalsky
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Olga S. Iungin
- D.K. Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Jessica Foster
- School of Science, Engineering and Technology, Abertay University, Dundee, United Kingdom
| | - Iryna V. Kosakivska
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee, United Kingdom
- * E-mail: (OM); (AS)
| |
Collapse
|
31
|
De Palma M, Salzano M, Villano C, Aversano R, Lorito M, Ruocco M, Docimo T, Piccinelli AL, D’Agostino N, Tucci M. Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum. HORTICULTURE RESEARCH 2019; 6:5. [PMID: 30603091 PMCID: PMC6312540 DOI: 10.1038/s41438-018-0079-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 05/13/2023]
Abstract
Beneficial interactions of rhizosphere microorganisms are widely exploited for plant biofertilization and mitigation of biotic and abiotic constraints. To provide new insights into the onset of the roots-beneficial microorganisms interplay, we characterised the transcriptomes expressed in tomato roots at 24, 48 and 72 h post inoculation with the beneficial fungus Trichoderma harzianum T22 and analysed the epigenetic and post-trascriptional regulation mechanisms. We detected 1243 tomato transcripts that were differentially expressed between Trichoderma-interacting and control roots and 83 T. harzianum transcripts that were differentially expressed between the three experimental time points. Interaction with Trichoderma triggered a transcriptional response mainly ascribable to signal recognition and transduction, stress response, transcriptional regulation and transport. In tomato roots, salicylic acid, and not jasmonate, appears to have a prominent role in orchestrating the interplay with this beneficial strain. Differential regulation of many nutrient transporter genes indicated a strong effect on plant nutrition processes, which, together with the possible modifications in root architecture triggered by ethylene/indole-3-acetic acid signalling at 72 h post inoculation may concur to the well-described growth-promotion ability of this strain. Alongside, T. harzianum-induced defence priming and stress tolerance may be mediated by the induction of reactive oxygen species, detoxification and defence genes. A deeper insight into gene expression and regulation control provided first evidences for the involvement of cytosine methylation and alternative splicing mechanisms in the plant-Trichoderma interaction. A model is proposed that integrates the plant transcriptomic responses in the roots, where interaction between the plant and beneficial rhizosphere microorganisms occurs.
Collapse
Affiliation(s)
- Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| | - Maria Salzano
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Matteo Lorito
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Michelina Ruocco
- Institute for Sustainable Plant Protection, National Research Council, 80055 Portici, Italy
| | - Teresa Docimo
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| | | | - Nunzio D’Agostino
- CREA, Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| |
Collapse
|
32
|
Mager S, Schönberger B, Ludewig U. The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss. BMC PLANT BIOLOGY 2018; 18:372. [PMID: 30587136 PMCID: PMC6307195 DOI: 10.1186/s12870-018-1603-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/12/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Zinc (Zn) is an essential micronutrient of all organisms. Deficiency of zinc causes disturbance in crucial plant functions, as a high number of enzymes, including transcription factors, depend on zinc for proper performance. The plant responses to zinc deficiency are associated with increased high affinity Zn uptake and translocation, as well as efficient usage of the remaining zinc, but have not been characterized in molecular detail in maize. RESULTS The high affinity transporter genes ZmZIP3,4,5,7 and 8 and nicotianamine synthases, primarily ZmNAS5, were identified as primary up-regulated in maize roots upon prolonged Zn deficiency. In addition to down-regulation of genes encoding enzymes involved in pathways regulating reactive oxygen species and cell wall-related genes, a massive up-regulation of the sucrose efflux channel genes SWEET13a,c was identified, despite that in -Zn sugar is known to accumulate in shoots. In addition, enzymes involved in DNA maintenance methylation tended to be repressed, which coincided with massively reduced DNA methylation in Zn-deficient roots. Reduced representation bisulfate sequencing, which revealed base-specific methylation patterns in ~ 14% of the maize genome, identified a major methylation loss in -Zn, mostly in transposable elements. However, hypermethylated genome regions in -Zn were also identified, especially in both symmetrical cytosine contexts. Differential methylation was partially associated with differentially expressed genes, their promoters, or transposons close to regulated genes. However, hypomethylation was associated with about equal number of up- or down-regulated genes, questioning a simple mechanistic relationship to gene expression. CONCLUSIONS The transcriptome of Zn-deficient roots identified genes and pathways to cope with the deficiency and a major down-regulation of reactive oxygen metabolism. Interestingly, a nutrient-specific loss of DNA methylation, partially related to gene expression in a context-specific manner, may play a role in long-term stress adaptation.
Collapse
Affiliation(s)
- Svenja Mager
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593 Stuttgart, Germany
| | - Brigitte Schönberger
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593 Stuttgart, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593 Stuttgart, Germany
| |
Collapse
|
33
|
Bedi S, Nag Chaudhuri R. Transcription factor
ABI
3 auto‐activates its own expression during dehydration stress response. FEBS Lett 2018; 592:2594-2611. [DOI: 10.1002/1873-3468.13194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sonia Bedi
- Department of Biotechnology St. Xavier's College Kolkata India
| | | |
Collapse
|
34
|
Suppression of External NADPH Dehydrogenase-NDB1 in Arabidopsis thaliana Confers Improved Tolerance to Ammonium Toxicity via Efficient Glutathione/Redox Metabolism. Int J Mol Sci 2018; 19:ijms19051412. [PMID: 29747392 PMCID: PMC5983774 DOI: 10.3390/ijms19051412] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 01/01/2023] Open
Abstract
Environmental stresses, including ammonium (NH4+) nourishment, can damage key mitochondrial components through the production of surplus reactive oxygen species (ROS) in the mitochondrial electron transport chain. However, alternative electron pathways are significant for efficient reductant dissipation in mitochondria during ammonium nutrition. The aim of this study was to define the role of external NADPH-dehydrogenase (NDB1) during oxidative metabolism of NH4+-fed plants. Most plant species grown with NH4+ as the sole nitrogen source experience a condition known as “ammonium toxicity syndrome”. Surprisingly, transgenic Arabidopsis thaliana plants suppressing NDB1 were more resistant to NH4+ treatment. The NDB1 knock-down line was characterized by milder oxidative stress symptoms in plant tissues when supplied with NH4+. Mitochondrial ROS accumulation, in particular, was attenuated in the NDB1 knock-down plants during NH4+ treatment. Enhanced antioxidant defense, primarily concerning the glutathione pool, may prevent ROS accumulation in NH4+-grown NDB1-suppressing plants. We found that induction of glutathione peroxidase-like enzymes and peroxiredoxins in the NDB1-surpressing line contributed to lower ammonium-toxicity stress. The major conclusion of this study was that NDB1 suppression in plants confers tolerance to changes in redox homeostasis that occur in response to prolonged ammonium nutrition, causing cross tolerance among plants.
Collapse
|
35
|
Miao R, Wang M, Yuan W, Ren Y, Li Y, Zhang N, Zhang J, Kronzucker HJ, Xu W. Comparative Analysis of Arabidopsis Ecotypes Reveals a Role for Brassinosteroids in Root Hydrotropism. PLANT PHYSIOLOGY 2018; 176:2720-2736. [PMID: 29439211 PMCID: PMC5884606 DOI: 10.1104/pp.17.01563] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/25/2018] [Indexed: 05/24/2023]
Abstract
Plant roots respond to soil moisture gradients and remodel their growth orientation toward water through hydrotropism, a process vital for acclimation to a changing soil environment. Mechanisms underlying the root hydrotropic response, however, remain poorly understood. Here, we examined hydrotropism in 31 Arabidopsis (Arabidopsis thaliana) ecotypes collected from different parts of the world and grown along moisture gradients in a specially designed soil-simulation system. Comparative transcriptome profiling and physiological analyses were carried out on three selected ecotypes, Wassilewskija (Ws), Columbia (Col-0) (strongly hydrotropic), Col-0 (moderately hydrotropic), and C24 (weakly hydrotropic), and in mutant lines with altered root hydrotropic responses. We show that H+ efflux, Ca2+ influx, redox homeostasis, epigenetic regulation, and phytohormone signaling may contribute to root hydrotropism. Among phytohormones, the role of brassinosteroids (BRs) was examined further. In the presence of an inhibitor of BR biosynthesis, the strong hydrotropic response observed in Ws was reduced. The root H+ efflux and primary root elongation also were inhibited when compared with C24, an ecotype that showed a weak hydrotropic response. The BR-insensitive mutant bri1-5 displayed higher rates of root growth inhibition and root curvature on moisture gradients in vertical or oblique orientation when compared with wild-type Ws. We also demonstrate that BRI1 (a BR receptor) interacts with AHA2 (a plasma membrane H+-ATPase) and that their expression patterns are highly coordinated. This synergistic action may contribute to the strong hydrotropism observed in Ws. Our results suggest that BR-associated H+ efflux is critical in the hydrotropic response of Arabidopsis roots.
Collapse
Affiliation(s)
- Rui Miao
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| | - Meng Wang
- Department of Biology, Hong Kong Baptist University, and Stake Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong
| | - Wei Yuan
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| | - Yan Ren
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| | - Ying Li
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| | - Na Zhang
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and Stake Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong
| | - Herbert J Kronzucker
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Weifeng Xu
- Center for Plant Water-Use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crops, Fujian Agriculture and Forestry University, Jinshan Fuzhou 350002, China
| |
Collapse
|
36
|
Annacondia ML, Magerøy MH, Martinez G. Stress response regulation by epigenetic mechanisms: changing of the guards. PHYSIOLOGIA PLANTARUM 2018; 162:239-250. [PMID: 29080251 DOI: 10.1111/ppl.12662] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/25/2017] [Accepted: 10/25/2017] [Indexed: 05/23/2023]
Abstract
Plants are sessile organisms that lack a specialized immune system to cope with biotic and abiotic stress. Instead, plants have complex regulatory networks that determine the appropriate distribution of resources between the developmental and the defense programs. In the last years, epigenetic regulation of repeats and gene expression has evolved as an important player in the transcriptional regulation of stress-related genes. Here, we review the current knowledge about how different stresses interact with different levels of epigenetic control of the genome. Moreover, we analyze the different examples of transgenerational epigenetic inheritance and connect them with the known features of genome epigenetic regulation. Although yet to be explored, the interplay between epigenetics and stress resistance seems to be a relevant and dynamic player of the interaction of plants with their environments.
Collapse
Affiliation(s)
- Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | | | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| |
Collapse
|
37
|
Kudoh H, Honjo MN, Nishio H, Sugisaka J. The Long-Term "In Natura" Study Sites of Arabidopsis halleri for Plant Transcription and Epigenetic Modification Analyses in Natural Environments. Methods Mol Biol 2018; 1830:41-57. [PMID: 30043363 DOI: 10.1007/978-1-4939-8657-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The majority of organismal phenomena show functional significance in the context of natural environments. However, we know little about how dynamic gene expression is controlled under natural complex conditions. One of the most attractive challenges in current biology is to understand organismal functions in natural environments. We established and have developed long-term "in natura" study sites of Arabidopsis halleri to evaluate precise control of gene expression in natural environments. At the sites, we monitored meteorological factors, recorded plant growth and phenology, and collected RNA and chromatin samples to investigate dynamics of transcription and epigenetic modifications. Here, we introduce the in natura study sites, especially with the emphasis on methodologies for setting up study sites in natural plant populations and collecting samples used in transcriptomics and epigenetics in natural environments. Although the methods introduced here need to be modified depending on situations of one's study systems, our case can be a model for planning new in natura studies.
Collapse
Affiliation(s)
- Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| |
Collapse
|
38
|
Weinhold A. Transgenerational stress-adaption: an opportunity for ecological epigenetics. PLANT CELL REPORTS 2018; 37:3-9. [PMID: 29032426 DOI: 10.1007/s00299-017-2216-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/04/2017] [Indexed: 05/14/2023]
Abstract
In the recent years, there has been considerable interest to investigate the adaptive transgenerational plasticity of plants and how a "stress memory" can be transmitted to the following generation. Although, increasing evidence suggests that transgenerational adaptive responses have widespread ecological relevance, the underlying epigenetic processes have rarely been elucidated. On the other hand, model plant species have been deeply investigated in their genome-wide methylation landscape without connecting this to the ecological reality of the plant. What we need is the combination of an ecological understanding which plant species would benefit from transgenerational epigenetic stress-adaption in their natural habitat, combined with a deeper molecular analysis of non-model organisms. Only such interdisciplinary linkage in an ecological epigenetic study could unravel the full potential that epigenetics could play for the transgenerational stress-adaption of plants.
Collapse
Affiliation(s)
- Arne Weinhold
- Applied Zoology/Animal Ecology, Dahlem Centre of Plant Sciences (DCPS), Institute of Biology, FU Berlin, Haderslebener Str. 9, 12163, Berlin, Germany.
| |
Collapse
|
39
|
Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress. PLANT PHYSIOLOGY 2017; 175:1893-1912. [PMID: 28986422 PMCID: PMC5717726 DOI: 10.1104/pp.17.00744] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/03/2017] [Indexed: 05/08/2023]
Abstract
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epi-alleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.
Collapse
Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| |
Collapse
|
40
|
Song Y, Liu L, Li G, An L, Tian L. Trichostatin A and 5-Aza-2'-Deoxycytidine influence the expression of cold-induced genes in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1389828. [PMID: 29027833 PMCID: PMC5703259 DOI: 10.1080/15592324.2017.1389828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The expression of cold-induced genes is critical for plants to survive under freezing stress. However, the underlying mechanisms for the decision of when, where, and which genes to express are unclear when a plant meets a sudden temperature drop. Previous studies have demonstrated epigenetics to play a central role in the regulation of gene expression in plant responses to environmental stress. DNA methylation and histone deacetylation are the two most important epigenetic modifications. This study was conducted to investigate the effects of inhibiting DNA methylation and histone deacetylation on gene expression, and to explore the potential role of epigenetics in plant responses to cold stress. The results revealed that histone deacetylase inhibitors (trichostatin A) and DNA methylation inhibitors (5-Aza-2'-deoxycytosine) treatment enhanced cold tolerance. DNA microarray analysis and the gene ontology method revealed 76 cold-induced differently expressed genes in Arabidopsis thaliana seedlings that were treated to 0°C for 24 h following Trichostatin A and 5-Aza-2'-Deoxycytidine. Furthermore, analyses of metabolic pathways and transcription factors of 3305 differentially expressed genes were performed. Each four metabolic pathways were significantly affected (p < 0.01) by Trichostatin A and 5-Aza-2'-Deoxycytidine. Finally, 10 genes were randomly selected and verified via qPCR analysis. Our study indicated that Trichostatin A and 5-Aza-2'-Deoxycytidine can improve the plant cold resistance and influence the expression of the cold-induced gene in A. thaliana. This result will advance our understanding of plant freezing responses and may provide a helpful strategy for cold tolerance improvement in crops.
Collapse
Affiliation(s)
- Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
| | - Lijun Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Gaopeng Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Gansu Province, Lanzhou, China
| | - Lining Tian
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, Canada, N5V4T3
- CONTACT Lining Tian ; Yuan Song Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, The South of Tianshui Road 222#, Lanzhou City, China Lanzhou 730000
| |
Collapse
|
41
|
Paul A, Dasgupta P, Roy D, Chaudhuri S. Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties. PLANT MOLECULAR BIOLOGY 2017; 95:63-88. [PMID: 28741224 DOI: 10.1007/s11103-017-0636-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 07/17/2017] [Indexed: 06/07/2023]
Abstract
Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties. Expression analysis indicates that the OsBZ8 gene is highly induced in Nonabokra plants even in the absence of salt stress, whereas in IR64, the expression significantly increases only during salt stress. Sequence analysis and nucleosomal arrangement within the region -2000 to +1000 of OsBZ8 gene show no difference between the two rice varieties. However, there was a considerable difference in histone modifications and DNA methylation at the locus between these varieties. In Nonabokra, the upstream region was hyperacetylated at H3K9 and H3K27, and this acetylation did not change during salt stress. However, in IR64, histone acetylation was observed only during salt stress. Moreover, the upstream region of OsBZ8 gene has highly dynamic nucleosome arrangement in Nonabokra, compared to IR64. Furthermore, loss of DNA methylation was observed at OsBZ8 locus in Nonabokra control plants along with low H3K27me3 and high H3K4me3. Control IR64 plants show high DNA methylation and enriched H3K27me3. Collectively these results indicate a significant difference in chromatin modifications between the rice varieties that regulates differential expression of OsBZ8 gene during salt stress.
Collapse
Affiliation(s)
- Amit Paul
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Pratiti Dasgupta
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Dipan Roy
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India.
| |
Collapse
|
42
|
Hofmeister BT, Lee K, Rohr NA, Hall DW, Schmitz RJ. Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biol 2017; 18:155. [PMID: 28814343 PMCID: PMC5559844 DOI: 10.1186/s13059-017-1288-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phenotypic diversity beyond changes to nucleotide sequence. Previous research has looked at the rate at which spontaneous epialleles arise but it is currently unknown how they are maintained across generations. RESULTS We used two Arabidopsis thaliana mutation accumulation (MA) lines and determined that over 99.998% of the methylated regions in the genome are stably inherited across each generation indicating that spontaneous epialleles are rare. We also developed a novel procedure that determines genotypes for offspring of genetically identical parents using only DNA methylation data. The resulting epigenotype maps are highly accurate and strongly agree with expected allele frequency and crossover number. Using epigenotype maps, we explore the inheritance of methylation states in regions of differential methylation between the parents of genetic crosses. Over half of the regions show methylation levels consistent with cis inheritance, whereas the other half show evidence of trans-chromosomal methylation and demethylation as well as other possibilities. CONCLUSIONS DNA methylation is stably inherited by offspring and spontaneous epialleles are rare. The epigenotyping procedure that we describe provides an important first step to epigenetic quantitative trait loci mapping in genetically identical individuals.
Collapse
Affiliation(s)
| | - Kevin Lee
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
43
|
Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. THE PLANT CELL 2017; 29:1836-1863. [PMID: 28705956 PMCID: PMC5590493 DOI: 10.1105/tpc.16.00828] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 05/19/2023]
Abstract
Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.
Collapse
Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Gonzalo M Estavillo
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- CSIRO Agriculture and Food, Black Mountain, Canberra ACT 2601, Australia
| | - Iain Searle
- School of Biological Sciences, The University of Adelaide, SA 5005, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
| | - Ozren Bogdanović
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| |
Collapse
|
44
|
Wang L, Kong D, Lv Q, Niu G, Han T, Zhao X, Meng S, Cheng Q, Guo S, Du J, Wu Z, Wang J, Bao F, Hu Y, Pan X, Xia J, Yuan D, Han L, Lian T, Zhang C, Wang H, He XJ, He YK. Tetrahydrofolate Modulates Floral Transition through Epigenetic Silencing. PLANT PHYSIOLOGY 2017; 174:1274-1284. [PMID: 28450424 PMCID: PMC5462009 DOI: 10.1104/pp.16.01750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/22/2017] [Indexed: 05/22/2023]
Abstract
Folates, termed from tetrahydrofolate (THF) and its derivatives, function as coenzymes in one-carbon transfer reactions and play a central role in synthesis of nucleotides and amino acids. Dysfunction of cellular folate metabolism leads to serious defects in plant development; however, the molecular mechanisms of folate-mediated cellular modifications and physiological responses in plants are still largely unclear. Here, we reported that THF controls flowering time by adjusting DNA methylation-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Wild-type seedlings supplied with THF as well as the high endogenous THF content mutant dihydrofolate synthetase folypoly-Glu synthetase homolog B exhibited significant up-regulation of the flowering repressor of Flowering Wageningen and thereby delaying floral transition in a dose-dependent manner. Genome-wide transcripts and DNA methylation profiling revealed that THF reduces DNA methylation so as to manipulate gene expression activity. Moreover, in accompaniment with elevated cellular ratios between monoglutamylated and polyglutamylated folates under increased THF levels, the content of S-adenosylhomo-Cys, a competitive inhibitor of methyltransferases, was obviously higher, indicating that enhanced THF accumulation may disturb cellular homeostasis of the concerted reactions between folate polyglutamylation and folate-dependent DNA methylation. In addition, we found that the loss-of-function mutant of CG DNA methyltransferase MET1 displayed much less responsiveness to THF-associated flowering time alteration. Taken together, our studies revealed a novel regulatory role of THF on epigenetic silencing, which will shed lights on the understanding of interrelations in folate homeostasis, epigenetic variation, and flowering control in plants.
Collapse
Affiliation(s)
- Lei Wang
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Dongdong Kong
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China;
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.);
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Qiang Lv
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Guoqi Niu
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Tingting Han
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Xuanchao Zhao
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Shulin Meng
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Qian Cheng
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Shouchun Guo
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Jing Du
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Zili Wu
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Jinzheng Wang
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Fang Bao
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Yong Hu
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Xiaojun Pan
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Jinchan Xia
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Dong Yuan
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Lida Han
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Tong Lian
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Chunyi Zhang
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Haiyang Wang
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Xin-Jian He
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| | - Yi-Kun He
- College of Life Sciences (L.W., D.K., Q.L., G.N., T.H., X.Z., S.M., Q.C., S.G., J.D., J.W., F.B., Y.H., X.P., J.X., Y.-k.H.) and Department of Chemistry (D.K.), Capital Normal University, Beijing 100048, China
- College of Life Science and Food Engineering, Yibin University, Yibin 644000, China (Z.W.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (D.Y., L.H., T.L., C.Z., H.W.); and
- National Institute of Biological Sciences, Beijing 102206, China (X.-J.H.)
| |
Collapse
|
45
|
Massoumi M, Krens FA, Visser RGF, De Klerk GJM. Azacytidine and miR156 promote rooting in adult but not in juvenile Arabidopsis tissues. JOURNAL OF PLANT PHYSIOLOGY 2017; 208:52-60. [PMID: 27889521 DOI: 10.1016/j.jplph.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 08/28/2016] [Accepted: 10/05/2016] [Indexed: 05/18/2023]
Abstract
Poor adventitious root (AR) formation is a major obstacle in micropropagation and conventional vegetative propagation of many crops. It is affected by many endogenous and exogenous factors. With respect to endogenous factors, the phase change from juvenile to adult has a major influence on AR formation and rooting is usually much reduced or even fully inhibited in adult tissues. It has been reported that the phase change is characterized by an increase in DNA-methylation and a decrease in the expression of microRNA156 (miR156). In this paper, we examined the effect of azacytidine (AzaC) and miR156 on AR formation in adult and juvenile Arabidopsis tissues. To identify the ontogenetic state researchers have used flowering or leaf morphology. We have used the rootability which allows - in contrast with both other characteristics- to examine the ontogenetic state at the cellular level. Overexpression of miR156 promoted only the rooting of adult tissues indicating that the phase change-associated loss in tissues' competence to develop ARs is also under the control of miR156. Azacytidine inhibits DNA methylation during DNA replication. Azacytidine treatment also promoted AR formation in nonjuvenile tissues but had no or little effect in juvenile tissues. Its addition during seedling growth (by which all tissues become hypomethylated) or during the rooting treatment (by which only those cells become hypomethylated that are generated after taking the explant) are both effective in the promotion of rooting. An AzaC treatment may be useful in tissue culture for crops that are recalcitrant to root.
Collapse
Affiliation(s)
- Mehdi Massoumi
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, the Netherlands.
| | - Frans A Krens
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, the Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, the Netherlands
| | - Geert-Jan M De Klerk
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ Wageningen, the Netherlands
| |
Collapse
|
46
|
Pietzenuk B, Markus C, Gaubert H, Bagwan N, Merotto A, Bucher E, Pecinka A. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biol 2016; 17:209. [PMID: 27729060 PMCID: PMC5059998 DOI: 10.1186/s13059-016-1072-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/23/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. RESULTS We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A. lyrata and A. thaliana. Heat-responsiveness of COPIA families is correlated with the presence of putative high affinity heat shock factor binding HREs within their long terminal repeats in seven Brassicaceae species. The strong HRE of ONSEN is conserved over millions of years and has evolved by duplication of a proto-HRE sequence, which was already present early in the evolution of the Brassicaceae. However, HREs of most families are species-specific, and in Boechera stricta, the ONSEN HRE accumulated mutations and lost heat-responsiveness. CONCLUSIONS Gain of HREs does not always provide an ultimate selective advantage for TEs, but may increase the probability of their long-term survival during the co-evolution of hosts and genomic parasites.
Collapse
Affiliation(s)
- Björn Pietzenuk
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Present address: Department of Plant Physiology, Ruhr-University Bochum, Bochum, Germany
| | - Catarine Markus
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540000, Brazil
| | - Hervé Gaubert
- Department of Plant Biology, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, 1211, Geneva 4, Switzerland
- Present address: The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Navratan Bagwan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Present address: Cardiovascular proteomics, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540000, Brazil
| | - Etienne Bucher
- UMR1345 IRHS, Université d'Angers, INRA, Université Bretagne Loire, SFR4207 QUASAV, 49045, Angers, France
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany.
| |
Collapse
|
47
|
Comparison of molecular genetic utilities of TD, AFLP, and MSAP among the accessions of japonica, indica, and Tongil of Oryza sativa L. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
48
|
Xu W, Wang T, Xu S, Li F, Deng C, Wu L, Wu Y, Bian P. UV-C-Induced alleviation of transcriptional gene silencing through plant-plant communication: Key roles of jasmonic acid and salicylic acid pathways. Mutat Res 2016; 790:56-67. [PMID: 27131397 DOI: 10.1016/j.mrfmmm.2016.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/04/2016] [Accepted: 04/18/2016] [Indexed: 05/22/2023]
Abstract
Plant stress responses at the epigenetic level are expected to allow more permanent changes of gene expression and potentially long-term adaptation. While it has been reported that plants subjected to adverse environments initiate various stress responses in their neighboring plants, little is known regarding epigenetic responses to external stresses mediated by plant-plant communication. In this study, we show that DNA repetitive elements of Arabidopsis thaliana, whose expression is inhibited epigenetically by transcriptional gene silencing (TGS) mechanism, are activated by UV-C irradiation through airborne plant-plant and plant-plant-plant communications, accompanied by DNA demethylation at CHH sites. Moreover, the TGS is alleviated by direct treatments with exogenous methyl jasmonate (MeJA) and methyl salicylate (MeSA). Further, the plant-plant and plant-plant-plant communications are blocked by mutations in the biosynthesis or signaling of jasmonic acid (JA) or salicylic acid (SA), indicating that JA and SA pathways are involved in the interplant communication for epigenetic responses. For the plant-plant-plant communication, stress cues are relayed to the last set of receiver plants by promoting the production of JA and SA signals in relaying plants, which exhibit upregulated expression of genes for JA and SA biosynthesis and enhanced emanation of MeJA and MeSA.
Collapse
Affiliation(s)
- Wei Xu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Ting Wang
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Shaoxin Xu
- School of physics and materials science, Anhui University, Hefei, Anhui, 230601, PR China
| | - Fanghua Li
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Chenguang Deng
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Lijun Wu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Yuejin Wu
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China
| | - Po Bian
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, P.O. Box 1138, Hefei, Anhui, 230031, PR China.
| |
Collapse
|
49
|
Lee S, Fu F, Xu S, Lee SY, Yun DJ, Mengiste T. Global Regulation of Plant Immunity by Histone Lysine Methyl Transferases. THE PLANT CELL 2016; 28:1640-61. [PMID: 27354553 PMCID: PMC4981126 DOI: 10.1105/tpc.16.00012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/25/2016] [Accepted: 06/24/2016] [Indexed: 05/17/2023]
Abstract
Posttranslational modification of histones modulates gene expression affecting diverse biological functions. We showed that the Arabidopsis thaliana histone methyl transferases SET DOMAIN GROUP8 (SDG8) and SDG25 regulate pep1-, flg22-, and effector-triggered immunity as well as systemic acquired resistance. Genome-wide basal and induced transcriptome changes regulated by SDG8 and/or SDG25 showed that two genes of the SDG-dependent transcriptome, CAROTENOID ISOMERASE2 (CCR2) and ECERIFERUM3 (CER3), were also required for plant immunity, establishing mechanisms in defense functions for SDG8 and SDG25. CCR2 catalyzes the biosynthesis of carotenoids, whereas CER3 is involved in the biosynthesis of cuticular wax. SDG8 and SDG25 affected distinct and overlapping global and locus-specific histone H3 lysine 4 (H3K4) and histone H3 lysine 36 (H3K36) methylations. Loss of immunity in sdg mutants was attributed to altered global and CCR2- and CER3-specific histone lysine methylation (HLM). Loss of immunity in sdg, ccr2, and cer3 mutants was also associated with diminished accumulation of lipids and loss of cuticle integrity. In addition, sdg8 and sdg25 mutants were impaired in H2B ubiquitination (H2Bubn) at CCR2, CER3, and H2Bubn regulated R gene, SNC1, revealing crosstalk between the two types of histone modifications. In summary, SDG8 and SDG25 contribute to plant immunity directly through HLM or indirectly through H2Bubn and by regulating expression of plant immunity genes, accumulation of lipids, biosynthesis of carotenoids, and maintenance of cuticle integrity.
Collapse
Affiliation(s)
- Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Siming Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK 21 Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK 21 Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| |
Collapse
|
50
|
Correlation between Ecological Plasticity of Elite Winter Wheat Varieties and DNA Methylation Pattern Polymorphism within Variety. SCIENCE AND INNOVATION 2016. [DOI: 10.15407/scine12.02.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|