Radiation-induced epigenetic bystander effects demonstrated in Arabidopsis thaliana

The role of signaling systems of plant in responding to key astrophysical factors: increased ionizing radiation, near-null magnetic field and microgravity

Plants will form the basis of artificial ecosystems in space exploration and the creation of bases on other planets. Astrophysical factors, such as ionizing radiation (IR), magnetic fields (MF) and gravity, can significantly affect the growth and development of plants beyond Earth. However, to date, the ways in which these factors influence plants remain largely unexplored. The review shows that, despite the lack of specialized receptors, plants are able to perceive changes in astrophysical factors. Potential mechanisms for perceiving changes in IR, MF and gravity levels are considered. The main pathway for inducing effects in plants is caused by primary physicochemical reactions and change in the levels of secondary messengers, including ROS and Ca2+. The presence of common components, including secondary messengers, in the chain of responses to astrophysical factors determines the complex nature of the response under their combined action. The analysis performed and the proposed hypothesis will help in planning space missions, as well as identifying the most important areas of research in space biology.

Stress Management in Plants: Examining Provisional and Unique Dose-Dependent Responses

The purpose of this review is to critically evaluate the effects of different stress factors on higher plants, with particular attention given to the typical and unique dose-dependent responses that are essential for plant growth and development. Specifically, this review highlights the impact of stress on genome instability, including DNA damage and the molecular, physiological, and biochemical mechanisms that generate these effects. We provide an overview of the current understanding of predictable and unique dose-dependent trends in plant survival when exposed to low or high doses of stress. Understanding both the negative and positive impacts of stress responses, including genome instability, can provide insights into how plants react to different levels of stress, yielding more accurate predictions of their behavior in the natural environment. Applying the acquired knowledge can lead to improved crop productivity and potential development of more resilient plant varieties, ensuring a sustainable food source for the rapidly growing global population.

Chronic Ionizing Radiation of Plants: An Evolutionary Factor from Direct Damage to Non-Target Effects

In present times, the levels of ionizing radiation (IR) on the surface of Earth are relatively low, posing no high challenges for the survival of contemporary life forms. IR derives from natural sources and naturally occurring radioactive materials (NORM), the nuclear industry, medical applications, and as a result of radiation disasters or nuclear tests. In the current review, we discuss modern sources of radioactivity, its direct and indirect effects on different plant species, and the scope of the radiation protection of plants. We present an overview of the molecular mechanisms of radiation responses in plants, which leads to a tempting conjecture of the evolutionary role of IR as a limiting factor for land colonization and plant diversification rates. The hypothesis-driven analysis of available plant genomic data suggests an overall DNA repair gene families' depletion in land plants compared to ancestral groups, which overlaps with a decrease in levels of radiation exposure on the surface of Earth millions of years ago. The potential contribution of chronic IR as an evolutionary factor in combination with other environmental factors is discussed.

Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms

As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.

Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes

BACKGROUND

The oxidation-reduction (redox) status of the cell influences or regulates transcription factors and enzymes involved in epigenetic changes, such as DNA methylation, histone protein modifications, and chromatin structure and remodeling. These changes are crucial regulators of chromatin architecture, leading to differential gene expression in eukaryotes. But the cell's redox homeostasis is difficult to sustain since the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) is not equal in plants at different developmental stages and under abiotic stress conditions. Exceeding optimum ROS and RNS levels leads to oxidative stress and thus alters the redox status of the cell. Consequently, this alteration modulates intracellular epigenetic modifications that either mitigate or mediate the plant growth and stress response.

AIM OF REVIEW

Recent studies suggest that the altered redox status of the cell reform the cellular functions and epigenetic changes. Recent high-throughput techniques have also greatly advanced redox-mediated gene expression discovery, but the integrated view of the redox status, and its associations with epigenetic changes and subsequent gene expression in plants are still scarce. In this review, we accordingly focus on how the redox status of the cell affects epigenetic modifications in plants under abiotic stress conditions and during developmental processes. This is a first comprehensive review on the redox status of the cell covering the redox components and signaling, redox status alters the post-translational modification of proteins, intracellular epigenetic modifications, redox interplay during DNA methylation, redox regulation of histone acetylation and methylation, redox regulation of miRNA biogenesis, redox regulation of chromatin structure and remodeling and conclusion, future perspectives and biotechnological opportunities for the future development of the plants.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The interaction of redox mediators such as ROS, RNS and antioxidants regulates redox homeostasis and redox-mediated epigenetic changes. We discuss how redox mediators modulate epigenetic changes and show the opportunities for smart use of the redox status of the cell in plant development and abiotic stress adaptation. However, how a redox mediator triggers epigenetic modification without activating other redox mediators remains yet unknown.

From Classical Radiation to Modern Radiation: Past, Present, and Future of Radiation Mutation Breeding

Radiation mutation breeding has been used for nearly 100 years and has successfully improved crops by increasing genetic variation. Global food production is facing a series of challenges, such as rapid population growth, environmental pollution and climate change. How to feed the world's enormous human population poses great challenges to breeders. Although advanced technologies, such as gene editing, have provided effective ways to breed varieties, by editing a single or multiple specific target genes, enhancing germplasm diversity through mutation is still indispensable in modern and classical radiation breeding because it is more likely to produce random mutations in the whole genome. In this short review, the current status of classical radiation, accelerated particle and space radiation mutation breeding is discussed, and the molecular mechanisms of radiation-induced mutation are demonstrated. This review also looks into the future development of radiation mutation breeding, hoping to deepen our understanding and provide new vitality for the further development of radiation mutation breeding.

Non-Targeted Effects of Synchrotron Radiation: Lessons from Experiments at the Australian and European Synchrotrons

Studies have been conducted at synchrotron facilities in Europe and Australia to explore a variety of applications of synchrotron X-rays in medicine and biology. We discuss the major technical aspects of the synchrotron irradiation setups, paying specific attention to the Australian Synchrotron (AS) and the European Synchrotron Radiation Facility (ESRF) as those best configured for a wide range of biomedical research involving animals and future cancer patients. Due to ultra-high dose rates, treatment doses can be delivered within milliseconds, abiding by FLASH radiotherapy principles. In addition, a homogeneous radiation field can be spatially fractionated into a geometric pattern called microbeam radiotherapy (MRT); a coplanar array of thin beams of microscopic dimensions. Both are clinically promising radiotherapy modalities because they trigger a cascade of biological effects that improve tumor control, while increasing normal tissue tolerance compared to conventional radiation. Synchrotrons can deliver high doses to a very small volume with low beam divergence, thus facilitating the study of non-targeted effects of these novel radiation modalities in both in-vitro and in-vivo models. Non-targeted radiation effects studied at the AS and ESRF include monitoring cell–cell communication after partial irradiation of a cell population (radiation-induced bystander effect, RIBE), the response of tissues outside the irradiated field (radiation-induced abscopal effect, RIAE), and the influence of irradiated animals on non-irradiated ones in close proximity (inter-animal RIBE). Here we provide a summary of these experiments and perspectives on their implications for non-targeted effects in biomedical fields.

Quantitative modeling of multigenerational effects of chronic ionizing radiation using targeted and nontargeted effects

Stress response signals can propagate between cells damaged by targeted effects (TE) of ionizing radiation (e.g. energy depositions and ionizations in the nucleus) and undamaged "bystander" cells, sometimes over long distances. Their consequences, called non-targeted effects (NTE), can substantially contribute to radiation-induced damage (e.g. cell death, genomic instability, carcinogenesis), particularly at low doses/dose rates (e.g. space exploration, some occupational and accidental exposures). In addition to controlled laboratory experiments, analysis of observational data on wild animal and plant populations from areas contaminated by radionuclides can enhance our understanding of radiation responses because such data span wide ranges of dose rates applied over many generations. Here we used a mechanistically-motivated mathematical model of TE and NTE to analyze published embryonic mortality data for plants (Arabidopsis thaliana) and rodents (Clethrionomys glareolus) from the Chernobyl nuclear power plant accident region. Although these species differed strongly in intrinsic radiosensitivities and post-accident radiation exposure magnitudes, model-based analysis suggested that NTE rather than TE dominated the responses of both organisms to protracted low-dose-rate irradiation. TE were predicted to become dominant only above the highest dose rates in the data. These results support the concept of NTE involvement in radiation-induced health risks from chronic radiation exposures.

REVIEW OF QUANTITATIVE MECHANISTIC MODELS OF RADIATION-INDUCED NON-TARGETED EFFECTS (NTE)

Quantitative mechanistic modeling of the biological effects of ionizing radiation has a long rich history. Initially, it was dominated by target theory, which quantifies damage caused by traversal of cellular targets like DNA by ionizing tracks. The discovery that mutagenesis, death and/or altered behavior sometimes occur in cells that were not themselves traversed by any radiation tracks but merely interacted with traversed cells was initially seen as surprising. As more evidence of such 'non-targeted' or 'bystander' effects accumulated, the importance of their contribution to radiation-induced damage became more recognized. Understanding and modeling these processes is important for quantifying and predicting radiation-induced health risks. Here we review the variety of mechanistic mathematical models of nontargeted effects that emerged over the past 2-3 decades. This review is not intended to be exhaustive, but focuses on the main assumptions and approaches shared or distinct between models, and on identifying areas for future research.

Redox Components: Key Regulators of Epigenetic Modifications in Plants

Epigenetic modifications including DNA methylation, histone modifications, and chromatin remodeling are crucial regulators of chromatin architecture and gene expression in plants. Their dynamics are significantly influenced by oxidants, such as reactive oxygen species (ROS) and nitric oxide (NO), and antioxidants, like pyridine nucleotides and glutathione in plants. These redox intermediates regulate the activities and expression of many enzymes involved in DNA methylation, histone methylation and acetylation, and chromatin remodeling, consequently controlling plant growth and development, and responses to diverse environmental stresses. In recent years, much progress has been made in understanding the functional mechanisms of epigenetic modifications and the roles of redox mediators in controlling gene expression in plants. However, the integrated view of the mechanisms for redox regulation of the epigenetic marks is limited. In this review, we summarize recent advances on the roles and mechanisms of redox components in regulating multiple epigenetic modifications, with a focus of the functions of ROS, NO, and multiple antioxidants in plants.

Synergistic Effect of Zinc Oxide Nanoparticles and Heat Stress on the Alleviation of Transcriptional Gene Silencing in Arabidopsis thaliana

Phytotoxicity is an inevitable consideration in evaluating the potential ecological effects of nanoparticles (NPs). Natural ecosystems are complex and accompanied by many other environmental factors. Thus understanding the impact of NPs on plant response to other environmental stresses is crucial to assess the comprehensive toxicity of NPs in ecosystem. In the present study, Arabidopsis thaliana seedlings were cultured in medium containing zinc oxide NPs (ZnO-NPs) then subjected to heat stress at 37°C. Alleviation of transcriptional gene silencing (TGS) in aerial leafy tissues was assessed as an epi-genotoxic endpoint. Results showed that 1 µg/mL ZnO-NPs alone can not alleviate GUS gene (β-glucuronidase) which silenced by TGS (TGS-GUS), but it significantly enhanced heat stress-induced alleviation of TGS-GUS, suggesting an synergistic effect of ZnO-NPs and heat stress on genomic instability. Further study showed that the initiation of synergistic effect could be regulated by plant developmental stage, heat duration and temperature, and heat shock related genes might be involved in.

Melatonin Modulates Regulation of NOX2 and NOX4 Following Irradiation in the Lung

Background:

Exposure to ionizing radiation may lead to chronic upregulation of inflammatory mediators and pro-oxidant enzymes, which give rise to continuous production of reactive oxygen species (ROS). NADPH oxidases are among the most important ROS producing enzymes. Their upregulation is associated with DNA damage and genomic instability. In the present study, we sought to determine the expressions of NADPH oxidases; NOX2 and NOX4, in rat’s lung following whole body or pelvis irradiation. In addition, we evaluated the protective effect of melatonin on the expressions of NOX2 and NOX4, as well as oxidative DNA injury.

Materials and Methods:

35 male rats were divided into 7 groups, G1: control; G2: melatonin (100 mg/kg) treatment; G3: whole body irradiation (2 Gy); G4: melatonin plus whole body irradiation; G5: local irradiation to pelvis area; G6: melatonin treatment plus 2 Gy gamma rays to pelvis area; G7: scatter group. All the rats were sacrificed after 24 h. afterwards, the expressions of TGFβR1, Smad2, NF- κB, NOX2 and NOX4 were detected using real-time PCR. Also, the level of 8-OHdG was detected by ELISA, and NOX2 and NOX4 protein levels were detected by western blot.

Results:

Whole body irradiation led to the upregulation of all genes, while local pelvis irradiation caused upregulation of TGFβR1, NF-κB, NOX2 and NOX4, as well as protein levels of NOX2 and NOX4. Treatment with melatonin reduced the expressions of these genes and also alleviated oxidative injury in both targeted and non-targeted lung tissues. Results also showed no significant reduction for NOX2 and NOX4 in bystander tissues following melatonin treatment.

Conclusion:

It is possible that upregulation of NOX2 and NOX4 is involved in radiation-induced targeted and non-targeted lung injury. Melatonin may reduce oxidative stress following upregulation of these enzymes in directly irradiated lung tissues but not for bystander.

Active DNA Demethylation in Plants

Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.

Current status of space radiobiological studies in China

After successfully launching two space laboratories, namely, Tiangong-1 and Tiangong-2, China has announced her next plan of constructing the Chinese Space Station (CSS) in 2022. The CSS will provide not only platforms for Chinese scientists to carry out experimental studies in outer space but also opportunities for open international cooperation. In this article, we review the development of China's manned space exploration missions and the preliminary plan for CSS. Additionally, China has initiated space radiation research decades ago with both ground-based simulation research platform and space vehicles and has made noticeable progresses in several aspects. These include studies on human health risk assessment using mammalian cell cultures and animals as models. Furthermore, there have been numerous studies on assessing the space environment in plant breeding.

Current evidence for a role of epigenetic mechanisms in response to ionizing radiation in an ecotoxicological context

The issue of potential long-term or hereditary effects for both humans and wildlife exposed to low doses (or dose rates) of ionising radiation is a major concern. Chronic exposure to ionising radiation, defined as an exposure over a large fraction of the organism's lifespan or even over several generations, can possibly have consequences in the progeny. Recent work has begun to show that epigenetics plays an important role in adaptation of organisms challenged to environmental stimulae. Changes to so-called epigenetic marks such as histone modifications, DNA methylation and non-coding RNAs result in altered transcriptomes and proteomes, without directly changing the DNA sequence. Moreover, some of these environmentally-induced epigenetic changes tend to persist over generations, and thus, epigenetic modifications are regarded as the conduits for environmental influence on the genome. Here, we review the current knowledge of possible involvement of epigenetics in the cascade of responses resulting from environmental exposure to ionising radiation. In addition, from a comparison of lab and field obtained data, we investigate evidence on radiation-induced changes in the epigenome and in particular the total or locus specific levels of DNA methylation. The challenges for future research and possible use of changes as an early warning (biomarker) of radiosensitivity and individual exposure is discussed. Such a biomarker could be used to detect and better understand the mechanisms of toxic action and inter/intra-species susceptibility to radiation within an environmental risk assessment and management context.

Effect of ionizing radiation on physiological and molecular processes in plants

The study of effects of ionizing radiation (IR) on plants is important in relation to several problems: (I) the existence of zones where background radiation - either natural or technogenic - is increased; (II) the problems of space biology; (III) the use of IR in agricultural selection; (IV) general biological problems related to the fundamental patterns and specifics of the effects of IR on various living organisms. By now, researchers have accumulated and systematized a large body of data on the effects of IR on the growth and reproduction of plants, as well as on the changes induced by IR at the genetic level. At the same time, there is a large gap in understanding the mechanisms of IR influence on the biochemical and physiological processes - despite the fact that these processes form the basis determining the manifestation of IR effects at the level of the whole organism. On the one hand, the activity of physiological processes determines the growth of plants; on the other, it is determined by changes at the genetic level. Thus, it is the study of IR effects at the physiological and biochemical levels that can give the most detailed and complex picture of IR action in plants. The review focuses on the effects of radiation on the essential physiological processes, including photosynthesis, respiration, long-distance transport, the functioning of the hormonal system, and various biosynthetic processes. On the basis of a large body of experimental data, we analyze dose and time dependences of the IR-induced effects - which are qualitatively similar - on various physiological and biochemical processes. We also consider the sequence of stages in the development of those effects and discuss their mechanisms, as well as the cause-effect relationships between them. The primary IR-induced physicochemical reactions include the formation of various forms of reactive oxygen species (ROS) and are the cause of the observed changes in the functional activity of plants. The review emphasizes the role of hydrogen peroxide, a long-lived ROS, not only as a damaging agent, but also as a mediator - a universal intracellular messenger, which provides for the mechanism of long-distance signaling. A supposition is made that IR affects physiological processes mainly by violating the regulation of their activity. The violation seems to become possible due to the fact that there exists a crosstalk between different signaling systems of plants, such as ROS, calcium, hormonal and electrical systems. As a result of both acute and chronic irradiation, an increase in the level of ROS can influence the activity of a wide range of physiological processes - by regulating them both at the genetic and physiological levels. To understand the ways, by which IR affects plant growth and development, one needs detailed knowledge about the mechanisms of the processes that occur at the (i) genetic and (ii) physiological levels, as well as their interplay and (iii) knowledge about regulation of these processes at different levels.

Negative Modulation of Bystander DNA Repair Potential by X-Ray Targeted Tissue Volume in Arabidopsis thaliana

Radiation-induced bystander effects (RIBE) entail a cascade of bystander signals produced by the hit cells to the neighboring cells to regulate various biological processes including DNA damage repair. However, there is little clarity regarding the effect of radiation-targeted volume (hit cell amount) on the DNA repair potential of the bystander cells. This is especially important to understand in the context of the whole organism, where the target usually consists of multiple types of cells/tissues. To address this question, model plant Arabidopsis thaliana was locally irradiated, and the DNA repair potential of bystander root-tip cells was assessed based on their radioresistance to subsequent high-dose radiation, i.e. radioadaptive responses (RAR). We found that X-ray irradiation of the aerial parts (AP) of A. thaliana seedlings (5 Gy) initiated RAR in the root-tip cells, which exhibited an alleviated repression of root growth and root cell division, and reduced amount of DNA strand breaks. We also observed an improvement in the repair efficiency of the homologous recombination (HR) and non-homologous end joining (NHEJ) pathways in the bystander root tip cells. We further expanded the X-ray targeted volume to include the aerial parts with upper parts of the primary root and compared it with X-ray irradiated aerial parts alone. Comparative analysis revealed that RAR for these end points either disappeared or decreased; specifically, the repair efficiency of HR was significantly reduced, indicating that radiation-targeted volume negatively modulates the bystander DNA repair potential. In contrast, X-ray irradiation of upper part of the primary root alone did not induce RAR of the root tip cells. Thus, we propose that additional X-ray irradiation of upper part of the primary root reduces the bystander DNA repair potential, possibly by selectively disturbing the transport of bystander signals responsible for HR repair.

A potential involvement of plant systemic response in initiating genotoxicity of Ag-nanoparticles in Arabidopsis thaliana

The extensive availability of engineered nanomaterials in global markets has led to the release of substantial amounts of nanoparticles (NP) into atmosphere, water body and soil, yielding both beneficial and harmful effects in plant systems. The NP are mainly aggregated onto the surface of plant roots and leaves exposed and only slightly transported into other tissues with a low rate of internalization. This raises a question of whether plant systemic response is involved in the induction of biological effects of NP. To address this, model plant Arabidopsis thaliana were root exposed to low concentrations of Ag-NP of two particle sizes (10-nm and 60-nm), and expressions of homologous recombination (HR)-related genes and the alleviation of transcriptional gene silencing (TGS) in aerial leafy tissues were examined as genotoxic endpoints. Results showed that exposure of roots to two sizes of Ag-NP up-regulated expressions of HR genes, and reactivated TGS-silenced repetitive elements in aerial tissues. These effects were blocked by the impairment in the salicylic acid signal pathway, indicating a potential involvement of plant systemic response in the induction of Ag-NP genotoxicity. This is further supported by ICP-MS analysis, in which the Ag content in aerial tissues was not significantly changed by root exposure to 10-nm Ag-NP. Although a significant increase in the Ag content in aerial tissues was observed after root exposure to 60-nm Ag-NP, its genotoxic effects had no obvious difference from that by 10-nm Ag-NP exposure, also suggesting that the genotoxicity might be mainly induced via plant systemic response, at least in the experiments of root exposure to Ag-NP.

Intercellular communications-redox interactions in radiation toxicity; potential targets for radiation mitigation

Nowadays, using ionizing radiation (IR) is necessary for clinical, agricultural, nuclear energy or industrial applications. Accidental exposure to IR after a radiation terror or disaster poses a threat to human. In contrast to the old dogma of radiation toxicity, several experiments during the last two recent decades have revealed that intercellular signaling and communications play a key role in this procedure. Elevated level of cytokines and other intercellular signals increase oxidative damage and inflammatory responses via reduction/oxidation interactions (redox system). Intercellular signals induce production of free radicals and inflammatory mediators by some intermediate enzymes such as cyclooxygenase-2 (COX-2), nitric oxide synthase (NOS), NADPH oxidase, and also via triggering mitochondrial ROS. Furthermore, these signals facilitate cell to cell contact and increasing cell toxicity via cohort effect. Nitric oxide is a free radical with ability to act as an intercellular signal that induce DNA damage and changes in some signaling pathways in irradiated as well as non-irradiated adjacent cells. Targeting of these mediators by some anti-inflammatory agents or via antioxidants such as mitochondrial ROS scavengers opens a window to mitigate radiation toxicity after an accidental exposure. Experiments which have been done so far suggests that some cytokines such as IL-1β, TNF-α, TGF-β, IL-4 and IL-13 are some interesting targets that depend on irradiated organs and may help mitigate radiation toxicity. Moreover, animal experiments in recent years indicated that targeting of toll like receptors (TLRs) may be more useful for radioprotection and mitigation. In this review, we aimed to describe the role of intercellular interactions in oxidative injury, inflammation, cell death and killing effects of IR. Moreover, we described evidence on potential mitigation of radiation injury via targeting of these mediators.

Genotoxicity of Zinc Oxide Nanoparticles in Plants Demonstrated Using Transgenic Arabidopsis thaliana

As important members of earth biosphere, higher plants are inevitably exposed to nanoparticles (NP) released into the environment. Therefore, determining NP-induced phytotoxicity is ecologically important. Currently, researches into genotoxic effects of NP on plants are limited. In this study, Arabidopsis thaliana lines transgenic for homologous recombination (HR) and transcriptional gene silencing (TGS) reporter genes were for the first time adopted to assess the genotoxicity of Zinc oxide NP (ZnO-NP). Results showed that the root exposure to ZnO-NP led to increased HR and alleviation of TGS in the aerial tissues, indicative of the genotoxicity of ZnO-NP in plants. The increased Zn content after root exposure to ZnO-NP and the similar induction of HR and TGS alleviation after root exposure to equivalent Zn ions suggested that the genotoxicity of ZnO-NP might be mainly induced by Zn ions in aerial tissues that were transported from decomposed ZnO-NP in either medium or plant roots.

Effect of modeled microgravity on UV-C-induced interplant communication of Arabidopsis thaliana

Controlled ecological life support systems (CELSS) will be an important feature of long-duration space missions of which higher plants are one of the indispensable components. Because of its pivotal role in enabling plants to cope with environmental stress, interplant communication might have important implications for the ecological stability of such CELSS. However, the manifestations of interplant communication in microgravity conditions have yet to be fully elucidated. To address this, a well-established Arabidopsis thaliana co-culture experimental system, in which UV-C-induced airborne interplant communication is evaluated by the alleviation of transcriptional gene silencing (TGS) in bystander plants, was placed in microgravity modeled by a two-dimensional rotating clinostat. Compared with plants under normal gravity, TGS alleviation in bystander plants was inhibited in microgravity. Moreover, TGS alleviation was also prevented when plants of the pgm-1 line, which are impaired in gravity sensing, were used in either the UV-C-irradiated or bystander group. In addition to the specific TGS-loci, interplant communication-shaped genome-wide DNA methylation in bystander plants was altered under microgravity conditions. These results indicate that interplant communications might be modified in microgravity. Time course analysis showed that microgravity interfered with both the production of communicative signals in UV-C-irradiated plants and the induction of epigenetic responses in bystander plants. This was further confirmed by the experimental finding that microgravity also prevented the response of bystander plants to exogenous methyl jasmonate (JA) and methyl salicylate (SA), two well-known airborne signaling molecules, and down-regulated JA and SA biosynthesis in UV-C-irradiated plants.

Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.

A pivotal role of the jasmonic acid signal pathway in mediating radiation-induced bystander effects in Arabidopsis thaliana

Although radiation-induced bystander effects (RIBE) in Arabidopsis thaliana have been well demonstrated in vivo, little is known about their underlying mechanisms, particularly with regard to the participating signaling molecules and signaling pathways. In higher plants, jasmonic acid (JA) and its bioactive derivatives are well accepted as systemic signal transducers that are produced in response to various environmental stresses. It is therefore speculated that the JA signal pathway might play a potential role in mediating radiation-induced bystander signaling of root-to-shoot. In the present study, pretreatment of seedlings with Salicylhydroxamic acid, an inhibitor of lipoxigenase (LOX) in JA biosynthesis, significantly suppressed RIBE-mediated expression of the AtRAD54 gene. After root irradiation, the aerial parts of A. thaliana mutants deficient in JA biosynthesis (aos) and signaling cascades (jar1-1) showed suppressed induction of the AtRAD54 and AtRAD51 genes and TSI and 180-bp repeats, which have been extensively used as endpoints of bystander genetic and epigenetic effects in plants. These results suggest an involvement of the JA signal pathway in the RIBE of plants. Using the root micro-grafting technique, the JA signal pathway was shown to participate in both the generation of bystander signals in irradiated root cells and radiation responses in the bystander aerial parts of plants. The over-accumulation of endogenous JA in mutant fatty acid oxygenation up-regulated 2 (fou2), in which mutation of the Two Pore Channel 1 (TPC1) gene up-regulates expression of the LOX and allene oxide synthase (AOS) genes, inhibited RIBE-mediated expression of the AtRAD54 gene, but up-regulated expression of the AtKU70 and AtLIG4 genes in the non-homologous end joining (NHEJ) pathway. Considering that NHEJ is employed by plants with increased DNA damage, the switch from HR to NHEJ suggests that over-accumulation of endogenous JA might enhance the radiosensitivity of plants in terms of RIBE.

UV-C-Induced alleviation of transcriptional gene silencing through plant-plant communication: Key roles of jasmonic acid and salicylic acid pathways

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.

Transcriptome Analysis of an Anthracnose-Resistant Tea Plant Cultivar Reveals Genes Associated with Resistance to Colletotrichum camelliae

Tea plant breeding is a topic of great economic importance. However, disease remains a major cause of yield and quality losses. In this study, an anthracnose-resistant cultivar, ZC108, was developed. An infection assay revealed different responses to Colletotrichum sp. infection between ZC108 and its parent cultivar LJ43. ZC108 had greater resistance than LJ43 to Colletotrichum camelliae. Additionally, ZC108 exhibited earlier sprouting in the spring, as well as different leaf shape and plant architecture. Microarray data revealed that the genes that are differentially expressed between LJ43 and ZC108 mapped to secondary metabolism-related pathways, including phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways. In addition, genes involved in plant hormone biosynthesis and signaling as well as plant-pathogen interaction pathways were also changed. Quantitative real-time PCR was used to examine the expression of 27 selected genes in infected and uninfected tea plant leaves. Genes encoding a MADS-box transcription factor, NBS-LRR disease-resistance protein, and phenylpropanoid metabolism pathway components (CAD, CCR, POD, beta-glucosidase, ALDH and PAL) were among those differentially expressed in ZC108.