Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

Editorial

21 November 2017

Editorial: Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

Mahmoud W. Yaish

5,508 views

34 citations

Editors

Mahmoud Yaish

Sultan Qaboos University

Heribert Hirt

King Abdullah University of Science and Technology

Barbara Hohn

Friedrich Miescher Institute for Biomedical Research (FMI)

Impact

Length distribution of sRNA in libraries prepared from the embryos of two genotypes of the full-sib family of Norway spruce from cross ♀#2650 × ♂#2707 produced in outdoor conditions—A2C and produced in greenhouse conditions—B10W. (A) averaged sRNA length distribution in all libraries; (B) sRNA length distribution in miRNA length range—19–27 bp in two genotypes.

Original Research

08 September 2017

In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce

Igor A. Yakovlev

and

Carl G. Fossdal

6,873 views

54 citations

(A) Examples of MSAP gels and (B) the total methylation levels, (C) variations occurred in CG and CHG sites in M1 generation after laser-irradiation. The arrows shows methylation variations.

Original Research

21 March 2017

Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice

Siyuan Li

, 7 more and

Bao Liu

5,421 views

19 citations

Hypothesis and Theory

31 August 2016

Epigenetic Memory as a Basis for Intelligent Behavior in Clonal Plants

Vít Latzel

, 1 more and

Jonathan Rosenthal

10,147 views

92 citations

Mini Review

11 August 2016

Epigenetic Control of Defense Signaling and Priming in Plants

Nino A. Espinas

, 1 more and

Yusuke Saijo

Immune recognition of pathogen-associated molecular patterns or effectors leads to defense activation at the pathogen challenged sites. This is followed by systemic defense activation at distant non-challenged sites, termed systemic acquired resistance (SAR). These inducible defenses are accompanied by extensive transcriptional reprogramming of defense-related genes. SAR is associated with priming, in which a subset of these genes is kept at a poised state to facilitate subsequent transcriptional regulation. Transgenerational inheritance of defense-related priming in plants indicates the stability of such primed states. Recent studies have revealed the importance and dynamic engagement of epigenetic mechanisms, such as DNA methylation and histone modifications that are closely linked to chromatin reconfiguration, in plant adaptation to different biotic stresses. Herein we review current knowledge regarding the biological significance and underlying mechanisms of epigenetic control for immune responses in plants. We also argue for the importance of host transposable elements as critical regulators of interactions in the evolutionary “arms race” between plants and pathogens.

20,542 views

138 citations

Schematic presentation of the PA biosynthetic pathways for Put, Spd, and Spm in plants and relationships with ethylene biosynthesis. ADC, arginine decarboxylase; CPA, N-carbamoylputrescine amidohydrolase; ADI, agmatine deaminase; DAO, diamine oxidase; PAO, polyamine oxidase; SAMDC, S-adenosylmethionine decarboxylase; dc-SAM, decarboxylated S-adenosylmethionine; SPDS, spermidine synthase; SPMS, spermine synthase; GABA, c-aminobutyric acid.

Original Research

17 August 2016

The Effect of Exogenous Spermidine Concentration on Polyamine Metabolism and Salt Tolerance in Zoysiagrass (Zoysia japonica Steud) Subjected to Short-Term Salinity Stress

Shucheng Li

, 1 more and

Qiang Zhang

8,327 views

98 citations

SnRK2 proteins of Populus trichocarpa (poplar, Pt), and Arabidopsis thaliana (Arabidopsis, At). (A) Amino acid sequence alignment of subclass 2 PtSnRK2 proteins with AtSnRK2.8. The residues putatively corresponding to the α-helix, β-sheet, PP2C-interaction residues, and the entire ABA box are marked by bars, arrows, asterisks, and the box, respectively. (B) In silico modeling of the three-dimensional structures of PtSnRK2.5, PtSnRK2.7, and PtSnRK2.9 proteins. Homology modeling was performed based on the crystal structure of AtSnRK2.6 using the web-based SWISS-MODEL service (http://swissmodel.expasy.org/workspace/; Arnold et al., 2006). Thick and narrow arrows indicate regions presumed to differ in their three-dimensional architecture among the PtSnRK2 proteins because of differences in amino acid sequences.

Original Research

09 May 2016

Heterologous Overexpression of Poplar SnRK2 Genes Enhanced Salt Stress Tolerance in Arabidopsis thaliana

Xueqing Song

, 4 more and

Qiang Zhuge

8,009 views

50 citations

Schematic depiction of mechanisms by which epigenetic inheritance may be maintained during DNA replication. As replication fork proceeds, (i) newly deposited histones are modified by protein complexes (e.g.: PRC2) targeted by inherited modifications on parental histones; (ii) DNA binding proteins recruit/repel modification protein complexes; (iii) cross-talk between the two complementary mechanisms is also possible. For simplicity, H3–H4 nucleosomes are depicted.

Mini Review

02 February 2016

Maintaining Epigenetic Inheritance During DNA Replication in Plants

Francisco M. Iglesias

and

Pablo D. Cerdán

12,933 views

18 citations

Trafficking of typical cross-kingdom small RNAs (sRNAs) involved with plants. Nine organisms are selected for depiction of cross-kingdom sRNAs involved with plants. Among them, three organisms of ‘Microbe’ column top-down are Influenza A viruses (IAV), CMV and Botrytis cinerea. Four organisms of ‘Plant’ column are Loniceraja ponica (L. ponica), Solanum lycopersicum, and Oryza sativa on the first line and Arabidopsis thaliana on the second line. Two organisms of ‘Animal’ column are Mus musculus (M. musculus) and Homo sapiens(H. sapiens). Cross-kingdom sRNAs are listed in Table 1. The arrows under the cross-kingdom sRNAs point to target species.

Mini Review

10 December 2015

Horizontal Transfer of Small RNAs to and from Plants

Lu Han

and

Yu-Shi Luan

11,495 views

27 citations

Changes in physiological and biochemical properties in response to abiotic stress. SOD superoxide dismutase, H2O2 hydrogen peroxide, MDA malondialdehyde, CAT catalase. 0 h indicates the control group without stress treatment. 3–24 h indicate different times of exposure to heat and cold stress. Error bars represent standard error. Activities are presented as mean ± SE, and n = 3. An asterisk indicates differences at ∗P < 0.05 compared with the control group, and two asterisks indicates significant differences at ∗∗P < 0.01 compared with the control group.

Original Research

30 October 2015

Methylation of miRNA genes in the response to temperature stress in Populus simonii

Dong Ci

, 2 more and

Deqiang Zhang

7,929 views

68 citations

Composition and function of the SAGA complex in plants. (A) Schematic representation of each module that integrates into the SAGA complex and its role in abiotic stress response. ND, not defined. (B–E) Schematic representation of molecular functions of the SAGA complex under abiotic stress. (B) ADA2b represses freezing tolerance before cold exposure. During cold exposure, CBFs are induced and together with ADA2b and GCN5 promotes COR genes induction and consequently freezing tolerance. (C) ADA2b represses drought tolerance whereas it promotes histone acetylation of salt stress responsive genes and confers salt tolerance. TAF10 promotes salt tolerance during seed germination, while SGF29a plays a modest role in the expression of salt stress responsive genes in arabidopsis. TFs, transcription factors. (D) GCN5 integrates both blue and red/far-red light signals to induce histone acetylation and HY5-dependent gene activation of light responsive genes. TAF1 integrates red/far-red light signals to induce histone acetylation and gene activation of light-responsive genes (adapted from Servet et al., 2010). (E) Under deficient iron conditions GCN5 promotes histone acetylation of FRD3, which is involved in the transport of Fe into the xylem, to regulate iron homeostasis.

Review

14 October 2015

Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses

Felipe Moraga

and

Felipe Aquea

13,761 views

58 citations

A model of the distance between epigenetic and genetic variation when epigenetic modifications accumulate following stress and are re-set between generations. Phenotypic variation is only visible above the gold, horizontal line. The distance between epigenetic modifications and accumulating genetic mutations is illustrated by the dashed lines.

Perspective

07 September 2015

Transgenerational inheritance or resetting of stress-induced epigenetic modifications: two sides of the same coin

Penny J. Tricker

10,709 views

47 citations

Mini Review

27 May 2015

Chromatin resetting mechanisms preventing transgenerational inheritance of epigenetic states

Mayumi Iwasaki

8,679 views

27 citations

Clustering of DNA methylation differences in plants subjected to abiotic stress. Hierarchical clustering (Wards method) was performed for the DMRs identified in stressed plants (A), control plants (B), or both stress and control plants (C). The heatmap uses red to indicate DNA methylation levels higher than the control average and blue to indicate lower DNA methylation levels. The samples are indicated at the bottom of each plot and the symbols indicate the treatment (green-control, blue-cold, red-heat, yellow-UV).

Original Research

06 May 2015

Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress

Steven R. Eichten

and

Nathan M. Springer

11,179 views

84 citations

Possible roles of the Elongator complex in plants. The currently available information suggests three possible roles for the Elongator complex in plants. In the nucleus, Elongator is associated with hyperphosphorylated RNA polymerase (RNAP II) and is required for histone acetylation and/or DNA demethylation/methylation at various genetic loci. On the other hand, Elongator may also regulate protein translation through tRNA modification in the cytoplasm.

Mini Review

29 April 2015

Elongator and its epigenetic role in plant development and responses to abiotic and biotic stresses

Yezhang Ding

and

Zhonglin Mou

9,746 views

29 citations

Proposed model integrating genetic and epigenetic controls of heat responses. Genes and proteins are represented in boxes and circles, respectively. The genes and proteins in color are involved in the epigenetic regulation of heat responses. The four putative heat sensors, H2A.Z, the calcium channel in the plasma membrane (CNGCs), two unfolded protein sensors in ER (ER-UPR) and the cytosol (Cyt-UPR), are indicated. The speculative regulatory paths are indicated with broken arrows. (A) Warm temperature mediates the morphological acclimation and acceleration of flowering. Under warm temperatures, the expression of PIF4 could be induced by the eviction of H2A.Z at its promoter. PIF4 binds to the promoters of target genes and plays a central role in the morphological acclimation and acceleration of flowering. Warm temperature also induces the transition from SVP-FLM-β to the competing SVP-FLM-δ complex, the latter is then released from the promoter of FT. The inhibition of ta-siRNAs (green box) through the down-regulation of SGS3 protein (red circle) by warm temperature may be also involved in the morphological acclimation. (B) The genetic mechanisms of temperature entrainment and temperature compensation are proposed. ELF3, PRR7 and PRR9 are involved in temperature entrainment, while CCA1, LHY, PRR7, PRR9, GI, CK2, RVE8, FBH1 and HsfB2b are proved to play roles in temperature compensation. Note that histone modifications of LHY, CCA1, TOC1, PRR7 and PRR9, such as H3K56ac, H3K9/14ac, H3K4me3 and H3K4me2, may (question mark) be regulated by high temperatures. (C) High temperature inhibits R genes-mediated ETI and enhances RNA-silencing mediated resistance. Reduced H2A.Z-containing nucleosome occupancy or other unknown mechanism are likely involved in the modulation of clock (B) and immunity (C). (D) Heat sensors and main signal transduction pathways in heat stress responses (HSR) are shown. Heat stress activates CNGCs, ER-UPR, and Cyt-UPR, and triggers signaling through multiple kinases as well as transcriptional regulators of the HSR, such as HSFs, MBF1c, and Rboh. RPS1 in the chloroplast also responds to heat stress, and generates a retrograde signal to activate HsfA2-dependent heat-responsive genes in the nucleus. Some csRNAs are highly sensitive to heat stress and may regulate RPS1-mediated heat stress responses. Heat stress also affects the production of some ra-siRNAs, miRNAs, ta-siRNAs, nat-siRNAs, and lncRNAs. These non-coding RNAs may regulate HSFs, HSPs, and other target genes that function in heat acclimation. The NRPD2 (olive box) and HDA6 (purple box)-dependent RdDM pathway and the CMT2 (gray box)-dependent CHH methylation may be required for thermotolerance. AtASF1A/B proteins (blue circle) are recruited onto chromatin and facilitate H3K56ac, which promotes the activation of some HSFs and HSPs. The chromatin-remodeling gene CHR12 (light purple box) plays a vital role in mediating the temporary growth arrest of Arabidopsis under heat stress. Repetitive heat stress has also been reported to modulate PTI in a HAC1 (yellow box)-dependent manner. Many unknown steps (?) remain to be recognized in this model.

Review

24 April 2015

Genetic and epigenetic control of plant heat responses

Junzhong Liu

, 2 more and

Zuhua He

Plants have evolved sophisticated genetic and epigenetic regulatory systems to respond quickly to unfavorable environmental conditions such as heat, cold, drought, and pathogen infections. In particular, heat greatly affects plant growth and development, immunity and circadian rhythm, and poses a serious threat to the global food supply. According to temperatures exposing, heat can be usually classified as warm ambient temperature (about 22–27°C), high temperature (27–30°C) and extremely high temperature (37–42°C, also known as heat stress) for the model plant Arabidopsis thaliana. The genetic mechanisms of plant responses to heat have been well studied, mainly focusing on elevated ambient temperature-mediated morphological acclimation and acceleration of flowering, modulation of circadian clock and plant immunity by high temperatures, and thermotolerance to heat stress. Recently, great progress has been achieved on epigenetic regulation of heat responses, including DNA methylation, histone modifications, histone variants, ATP-dependent chromatin remodeling, histone chaperones, small RNAs, long non-coding RNAs and other undefined epigenetic mechanisms. These epigenetic modifications regulate the expression of heat-responsive genes and function to prevent heat-related damages. This review focuses on recent progresses regarding the genetic and epigenetic control of heat responses in plants, and pays more attention to the role of the major epigenetic mechanisms in plant heat responses. Further research perspectives are also discussed.

39,592 views

257 citations