Microarray analysis of genes that respond to gamma-irradiation in Arabidopsis

Reactive oxygen species may be involved in the distinctive biological effects of different doses of 12C6+ ion beams on Arabidopsis

Introduction

Heavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated by an increase in root and biomass, while 200 Gy irradiation significantly inhibited the growth of seedlings, causing a visible decrease in plant growth.

Methods

The Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels.

Results and discussion

Monte Carlo simulations revealed that high-dose irradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170 DEGs were present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cell wall homeostasis. Further GO enrichment of DEGs unique to 50 Gy and 200 Gy revealed 58 50Gy-exclusive DEGs were enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advances our insight into the biological effects of heavy ion irradiation and the underlying mechanisms.

Glucosinolate O-methyltransferase mediated callus formation and affected ROS homeostasis in Arabidopsis thaliana

Auxin-induced callus formation was largely dependent on the function of Lateral Organ Boundaries Domain (LBD) family transcription factors. We previously revealed that two IGMT (Indole glucosinolate oxy-methyl transferase) genes, IGMT2 and IGMT3, may be involved in the callus formation process as potential target genes of LBD29. Overexpression of the IGMT genes induces spontaneous callus formation. However, the details of the IGMT involvement in callus formation process were not well studied. IGMT1-4, but not IGMT5, are targeted and induced by LBD29 during the early stage of callus formation. Cell membrane and nucleus localized IGMT3 was mainly expressed in the elongation and maturation zones tissues of the primary root and lateral root, which could be further accumulated after CIM treatment. The igmts quadruple mutant, which obtained by CRISPR/Cas9 technology, exhibits a phenotype of attenuated callus formation. Enhanced indole glucosinolate anabolic pathway caused by IGMT1-4 overexpression promotes callus formation. In addition, the IGMT genes were involved in the reactive oxygen species homeostasis, which could be responsible for its role on callus formation. This study provides novel insights into the role of IGMTs gene-mediated callus formation. Activation of the Indole glucosinolate anabolic pathway is an inducing factor for plant callus initiation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01409-2.

Are Arabidopsis thaliana plants able to recover from exposure to gamma radiation? A molecular perspective

Most plant research focuses on the responses immediately after exposure to ionizing irradiation (IR). However, it is as important to investigate how plants recover after exposure since this has a profound effect on future plant growth and development and hence on the long-term consequences of exposure to stress. This study aimed to investigate the IR-induced responses after exposure and during recovery by exposing 1-week old A. thaliana seedlings to gamma dose rates ranging from 27 to 103.7 mGy/h for 2 weeks and allowing them to recover for 4 days. A high-throughput RNAsequencing analysis was carried out. An enrichment of GO terms related to the metabolism of hormones was observed both after irradiation and during recovery at all dose rates. While plants exposed to the lowest dose rate activate defence responses after irradiation, they recover from the IR by resuming normal growth during the recovery period. Plants exposed to the intermediate dose rate invest in signalling and defence after irradiation. During recovery, in the plants exposed to the highest dose rate, fundamental metabolic processes such as photosynthesis and RNA modification were still affected. This might lead to detrimental effects in the long-term or in the next generations of those irradiated plants.

Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells

Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.

Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants

Plants orchestrate various DNA damage responses (DDRs) to overcome the deleterious impacts of genotoxic agents on genetic materials. Ionizing radiation (IR) is widely used as a potent genotoxic agent in plant DDR research as well as plant breeding and quarantine services for commercial uses. This review aimed to highlight the recent advances in cellular and phenotypic DDRs, especially those induced by IR. Various physicochemical genotoxic agents damage DNA directly or indirectly by inhibiting DNA replication. Among them, IR-induced DDRs are considerably more complicated. Many aspects of such DDRs and their initial transcriptomes are closely related to oxidative stress response. Although many key components of DDR signaling have been characterized in plants, DDRs in plant cells are not understood in detail to allow comparison with those in yeast and mammalian cells. Recent studies have revealed plant DDR signaling pathways including the key regulator SOG1. The SOG1 and its upstream key components ATM and ATR could be functionally characterized by analyzing their knockout DDR phenotypes after exposure to IR. Considering the potent genotoxicity of IR and its various DDR phenotypes, IR-induced DDR studies should help to establish an integrated model for plant DDR signaling pathways by revealing the unknown key components of various DDRs in plants.

SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis

To combat DNA damage, organisms mount a DNA damage response (DDR) that results in cell cycle regulation, DNA repair and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all of the aforementioned processes rely on SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a NAC family transcription factor (TF) that has been functionally equated to the mammalian tumor suppressor, p53. However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data correspond to single time-point snapshots. Here, we generated transcriptional models of the DDR from GAMMA (γ)-irradiated wild-type and sog1 seedlings during a 24-hour time course using DREM, the Dynamic Regulatory Events Miner, revealing 11 coexpressed gene groups with distinct biological functions and cis-regulatory features. Within these networks, additional chromatin immunoprecipitation and transcriptomic experiments revealed that SOG1 is the major activator, directly targeting the most strongly up-regulated genes, including TFs, repair factors, and early cell cycle regulators, while three MYB3R TFs are the major repressors, specifically targeting the most strongly down-regulated genes, which mainly correspond to G2/M cell cycle-regulated genes. Together these models reveal the temporal dynamics of the transcriptional events triggered by γ-irradiation and connects these events to TFs and biological processes over a time scale commensurate with key processes coordinated in response to DNA damage, greatly expanding our understanding of the DDR.

Lemna minor plants chronically exposed to ionising radiation: RNA-seq analysis indicates a dose rate dependent shift from acclimation to survival strategies

Ecotoxicological research provides knowledge on ionising radiation-induced responses in different plant species. However, the sparse data currently available are mainly extracted from acute exposure treatments. To provide a better understanding of environmental exposure scenarios, the response to stress in plants must be followed in more natural relevant chronic conditions. We previously showed morphological and biochemical responses in Lemna minor plants continuously exposed for 7days in a dose-rate dependent manner. In this study responses on molecular (gene expression) and physiological (photosynthetic) level are evaluated in L. minor plants exposed to ionising radiation. To enable this, we examined the gene expression profiles of irradiated L. minor plants by using an RNA-seq approach. The gene expression data reveal indications that L. minor plants exposed at lower dose rates, can tolerate the exposure by triggering acclimation responses. In contrast, at the highest dose rate tested, a high number of genes related to antioxidative defense systems, DNA repair and cell cycle were differentially expressed suggesting that only high dose rates of ionising radiation drive L. minor plants into survival strategies. Notably, the photosynthetic process seems to be unaffected in L. minor plants among the tested dose rates. This study, supported by our earlier work, clearly indicates that plants shift from acclimation responses towards survival responses at increasing dose rates of ionising radiation.

Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings

Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.

DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent

Induction and mobilization of transposable elements (TEs) following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs (lncRNAs), many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and lncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild-type (WT) and ataxia telangiectasia mutated (atm) mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is ≥2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cycle is largely lost. In contrast, only less than 0.6% of TEs and lncRNAs respond to DNA damage in WT plants, and the regulation of ≥95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and lncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and lncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and lncRNAs located close to genes commonly function as controlling elements.

Irradiation with low-dose gamma ray enhances tolerance to heat stress in Arabidopsis seedlings

Gamma irradiation at low doses can stimulate the tolerance to environmental stress in plants. However, the knowledge regarding the mechanisms underlying the enhanced tolerance induced by low-dose gamma irradiation is far from fully understood. In this study, to investigate the physiological and molecular mechanisms of heat stress alleviated by low-dose gamma irradiation, the Arabidopsis seeds were exposed to a range of doses before subjected to heat treatment. Our results showed that 50-Gy gamma irradiation maximally promoted seedling growth in response to heat stress. The production rate of superoxide radical and contents of hydrogen peroxide and malondialdehyde in the seedlings irradiated with 50-Gy dose under heat stress were significantly lower than those of controls. The activities of antioxidant enzymes, glutathione (GSH) content and proline level in the gamma-irradiated seedlings were significantly increased compared with the controls. Furthermore, transcriptional expression analysis of selected genes revealed that some components related to heat tolerance were stimulated by low-dose gamma irradiation under heat shock. Our results suggest that low-dose gamma irradiation can modulate the physiological responses as well as gene expression related to heat tolerance, thus alleviating the stress damage in Arabidopsis seedlings.

Physiological changes and anti-oxidative responses of Arabidopsis plants after acute and chronic γ-irradiation

To identify the effects of acute and chronic γ-irradiation in Arabidopsis plants, physiological responses and antioxidant-related gene expression were investigated. Seedlings were exposed to 200 Gy of γ-irradiation in acute manner for 1 or 24 h (A1 and A24) or in chronic manner for 1, 2, or 3 weeks (C1 W, C2 W, and C3 W). Plant height, silique number, and silique length in A1 and A24 irradiated plants were significantly reduced when compared to non-irradiated plants. Silique number decreased in response to both acute and chronic irradiation, except with the C3 W treatment, and the number of trichomes dramatically increased in A1 and C1 W. Electron spin resonance signal intensities increased in A1 and in all chronically irradiated plants, but decreased in the A24-treated plant. To investigate the effects of acute and chronic γ-irradiation on antioxidant enzymes, we examined activity of four antioxidant enzymes: catalase (CAT), peroxidase (POD), ascorbate peroxidase, and superoxide dismutase. In general, POD and CAT activities decreased in response to acute and chronic γ-irradiation. Oligonucleotide microarrays were used to investigate transcriptional changes after irradiation. Several genes related to reactive oxygen species signaling were up-regulated after acute and chronic exposure, including genes encoding heat shock factors, zinc finger proteins, NADPH oxidase, WRKY DNA-binding proteins, and calcium binding proteins. Taken together, our data indicate that the responses and activation of antioxidant systems prompted by irradiation exposure are dependent upon the γ-ray dose rate.

Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks

Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pathways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and protein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.

Physiological and molecular characterization of the enhanced salt tolerance induced by low-dose gamma irradiation in Arabidopsis seedlings

It has been established that gamma rays at low doses stimulate the tolerance to salt stress in plants. However, our knowledge regarding the molecular mechanism underlying the enhanced salt tolerance remains limited. In this study, we found that 50-Gy gamma irradiation presented maximal beneficial effects on germination index and root length in response to salt stress in Arabidopsis seedlings. The contents of H2O2 and MDA in irradiated seedlings under salt stress were significantly lower than those of controls. The activities of antioxidant enzymes and proline levels in the irradiated seedlings were markedly increased compared with the controls. Furthermore, transcriptional expression analysis of selected genes revealed that some components of salt stress signaling pathways were stimulated by low-dose gamma irradiation under salt stress. Our results suggest that gamma irradiation at low doses alleviates the salt stress probably by modulating the physiological responses as well as stimulating the stress signal transduction in Arabidopsis seedlings.

Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana

Biochemical and physiological processes in plants are affected by gamma-irradiation, which causes significant changes in gene transcripts and expression. To identify the differentially expressed Arabidopsis genes in response to gamma-irradiation, we performed a microarray analysis with rosette leaves during the vegetative stage. Arabidopsis plants were exposed to a wide spectrum doses of gamma ray (100, 200, 300, 400, 800, 1200, 1600 or 2000 Gy) for 24 h. At the dose range from 100 to 400 Gy, irradiated plants were found to be shorter than controls after 8 days of irradiation, while doses over 800 Gy caused severe growth retardation. Therefore, 100 and 800 Gy were selected as adequate doses for microarray analysis to identify differentially expressed genes. Among the 20,993 genes used as microarray probes, a total number of 496 and 1,042 genes were up-regulated and down-regulated by gamma-irradiation, respectively (P < 0.05). We identified the characteristics of the genes that were up-and down-regulated fourfold higher genes by gamma irradiation according to The arabidopsis information resource gene ontology. To confirm the microarray results, we performed a northern blot and quantitative real-time PCR with several selected genes that had a large difference in expression after irradiation. In particular, genes associated with lipid transfer proteins, histones and transposons were down-regulated by 100 and/or 800 Gy of gamma irradiation. The expression patterns of selected genes were generally in agreement with the microarray results, although there were quantitative differences in the expression levels.

The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.

γ irradiation with different dose rates induces different DNA damage responses in Petunia x hybrida cells

In plants, there is evidence that different dose rate exposures to gamma (γ) rays can cause different biological effects. The dynamics of DNA damage accumulation and molecular mechanisms that regulate recovery from radiation injury as a function of dose rate are poorly explored. To highlight dose-rate dependent differences in DNA damage, single cell gel electrophoresis was carried out on regenerating Petunia x hybrida leaf discs exposed to LDR (total dose 50 Gy, delivered at 0.33 Gy min(-1)) and HDR (total doses 50 and 100 Gy, delivered at 5.15 Gy min(-1)) γ-ray in the 0-24h time period after treatments. Significant fluctuations of double strand breaks and different repair capacities were observed between treatments in the 0-4h time period following irradiation. Dose-rate-dependent changes in the expression of the PhMT2 and PhAPX genes encoding a type 2 metallothionein and the cytosolic isoform of ascorbate peroxidase, respectively, were detected by Quantitative RealTime-Polymerase Chain Reaction. The PhMT2 and PhAPX genes were significantly up-regulated (3.0- and 0.7-fold) in response to HDR. The results are discussed in light of the potential practical applications of LDR-based treatments in mutation breeding.

Suppression of Ku70/80 or Lig4 leads to decreased stable transformation and enhanced homologous recombination in rice

Evidence for the involvement of the nonhomologous end joining (NHEJ) pathway in Agrobacterium-mediated transferred DNA (T-DNA) integration into the genome of the model plant Arabidopsis remains inconclusive. Having established a rapid and highly efficient Agrobacterium-mediated transformation system in rice (Oryza sativa) using scutellum-derived calli, we examined here the involvement of the NHEJ pathway in Agrobacterium-mediated stable transformation in rice. Rice calli from OsKu70, OsKu80 and OsLig4 knockdown (KD) plants were infected with Agrobacterium harboring a sensitive emerald luciferase (LUC) reporter construct to evaluate stable expression and a green fluorescent protein (GFP) construct to monitor transient expression of T-DNA. Transient expression was not suppressed, but stable expression was reduced significantly, in KD plants. Furthermore, KD-Ku70 and KD-Lig4 calli exhibited an increase in the frequency of homologous recombination (HR) compared with control calli. In addition, suppression of OsKu70, OsKu80 and OsLig4 induced the expression of HR-related genes on treatment with DNA-damaging agents. Our findings suggest strongly that NHEJ is involved in Agrobacterium-mediated stable transformation in rice, and that there is a competitive and complementary relationship between the NHEJ and HR pathways for DNA double-strand break repair in rice.

Kinetic transcriptomic approach revealed metabolic pathways and genotoxic-related changes implied in the Arabidopsis response to ionising radiations

Plants exposed to ionising radiation (IR) have to face direct and indirect (oxidative stress) deleterious effects whose intensity depends on the dose applied and led to differential genome regulation. Transcriptomic analyses were conducted with CATMA microarray technology on Arabidopsis thaliana plantlets, 2 and 26h after exposure to the IR doses 10Gy and 40Gy. 10Gy treatment seemed to enhance antioxidative compound biosynthetic pathways whereas the 40Gy dose up-regulated ROS-scavenging enzyme genes. Transcriptomic data also highlighted a differential regulation of chloroplast constituent genes depending on the IR dose, 10Gy stimulating and 40Gy down-regulating. This probable 40Gy decrease of photosynthesis could help for the limitation of ROS production and may be coupled with programmed cell death (PCD)/senescence phenomena. Comparisons with previous transcriptomic studies on plants exposed to a 100Gy dose revealed 60 dose-dependent up-regulated genes, including notably cell cycle checkpoints to allow DNA repairing phenomena. Furthermore, the alteration of some cellular structure related gene expression corroborated a probable mitotic arrest after 40Gy. Finally, numerous heat-shock protein and chaperonin genes, known to protect proteins against stress-dependent dysfunction, were up-regulated after IR exposure.

CK2-defective Arabidopsis plants exhibit enhanced double-strand break repair rates and reduced survival after exposure to ionizing radiation

The multifunctional protein kinase CK2 is involved in several aspects of the DNA damage response (DDR) in mammals. To gain insight into the role of CK2 in plant genome maintenance, we studied the response to genotoxic agents of an Arabidopsis CK2 dominant-negative mutant (CK2mut plants). CK2mut plants were hypersensitive to a wide range of genotoxins that produce a variety of DNA lesions. However, they were able to activate the DDR after exposure to γ irradiation, as shown by accumulation of phosphorylated histone H2AX and up-regulation of sets of radio-modulated genes. Moreover, functional assays showed that mutant plants quickly repair the DNA damage produced by genotoxins, and that they exhibit preferential use of non-conservative mechanisms, which may explain plant lethality. The chromatin of CK2mut plants was more sensitive to digestion with micrococcal nuclease, suggesting compaction changes that agreed with the transcriptional changes detected for a number of genes involved in chromatin structure. Furthermore, CK2mut plants were prone to transcriptional gene silencing release upon genotoxic stress. Our results suggest that CK2 is required in the maintenance and control of genomic stability and chromatin structure in plants, and that this process affects several functions, including the DNA damage response and DNA repair.

Antioxidant response of Arabidopsis plants to gamma irradiation: Genome-wide expression profiling of the ROS scavenging and signal transduction pathways

Arabidopsis presumably has few sensors for gamma-rays and few signal transduction systems that respond to them. In an effort to assess their radiation sensitivity, wild-type (Ler) Arabidopsis plants were irradiated with various doses of gamma-rays at the vegetative (VE) and reproductive (RE) stages. 100Gy treatment induced the higher production of siliques during both the VE and RE stages compared with non-irradiation. Treatments at doses over 200Gy repressed shoot growth, and the plants perished under 800Gy treatment. The results of physiological analysis using electron spin resonance (ESR) and transmission electron microscopy (TEM) revealed that increased doses of gamma-rays induce greater ROS generation. To establish the gene expression profiles after gamma irradiation and for an analysis of the antioxidant response, we employed an oligonucleotide microarray system. Different responses of genes related with ROS scavenging and signal transduction pathways by a gamma irradiation were observed. At least 33 and 42 out of all genes with significantly altered expression were associated with ROS scavenging and signal transduction pathways having an induction or repression ratio cutoff of at least 2-fold, respectively. CAT3 (At1g20620), Ferritin1 (At5g01600), Blue copper binding protein (At5g20230), and AOX putative (At1g32350) were up-regulated regardless of dosage at the VE stage. Reactive oxygen species signaling genes encoding phospholipase, zinc finger protein, WRKY DNA-binding protein, and calcium binding protein were highly expressed, evidencing changes greater than 2-fold. Our transcriptomic profile of the responses of Arabidopsis genes to gamma irradiation showed that plants evidenced altered expressions of many signal transduction and antioxidant genes, as have been seen with other environmental stresses.

Photosynthetic capacity of Arabidopsis plants at the reproductive stage tolerates γ irradiation

The developmental stage has an influence on the overall responses of plants under biotic or abiotic stress conditions. However, there is a lack of data about the effects of ionizing radiation in plants at different developmental stages. We examined radiation sensitivity of Arabidopsis plants in terms of photosynthetic ability and oxidative stress resistance at two distinct vegetative and reproductive stages, which correspond to 23 and 43 d after seeding (DAS), respectively. When plants were exposed to γ rays at a dose rate 50 Gy h(-1) for 4 h, they were characterized as various common or differential cellular responses depending on the developmental stage. Radial expansion of leaves, inhibition of non-photochemical quenching, and production of •O(2)(-) and H(2)O(2) under methyl viologen-induced photooxidative stress were commonly more conspicuous in the irradiated leaves of both plants than in the respective control. In contrast, the 23 and 43-DAS plants were explicitly discriminated in growth, chloroplast number & ultrastructure, photosynthetic pigment content & activity, and protein damage after γ irradiation. Natural leaf senescence was thereby enhanced in the irradiated leaves of the 23-DAS plants, while it was reversely alleviated in those of the 43-DAS ones. These results suggest that photosynthetic machineries of Arabidopsis plants at the reproductive stage can be relatively tolerant to γ rays of 200 Gy.

The combined effect of uranium and gamma radiation on biological responses and oxidative stress induced in Arabidopsis thaliana

Uranium never occurs as a single pollutant in the environment, but always in combination with other stressors such as ionizing radiation. As effects induced by multiple contaminants can differ markedly from the effects induced by the individual stressors, this multiple pollution context should not be neglected. In this study, effects on growth, nutrient uptake and oxidative stress induced by the single stressors uranium and gamma radiation are compared with the effects induced by the combination of both stressors. By doing this, we aim to better understand the effects induced by the combined stressors but also to get more insight in stressor-specific response mechanisms. Eighteen-day-old Arabidopsis thaliana seedlings were exposed for 3 days to 10 muM uranium and 3.5 Gy gamma radiation. Gamma radiation interfered with uranium uptake, resulting in decreased uranium concentrations in the roots, but with higher transport to the leaves. This resulted in a better root growth but increased leaf lipid peroxidation. For the other endpoints studied, effects under combined exposure were mostly determined by uranium presence and only limited influenced by gamma presence. Furthermore, an important role is suggested for CAT1/2/3 gene expression under uranium and mixed stressor conditions in the leaves.

Neutron irradiation affects the expression of genes involved in the response to auxin, senescence and oxidative stress in Arabidopsis

We report, in Arabidopsis thaliana plants, the effect of neutron irradiation on the transcription of a set of genes belonging to different physiological groups: auxin action, senescence, oxidative stress, and some aspects of photosynthesis. The results indicated that, in the wild-types, the effect on the ARF1, ARF2, and 19 genes was of down-regulation, whereas of the tested AUX/IAA only AUX/IAA7 showed up-regulation. Different results were obtained as regards the irradiation of the auxin transport mutants aux1 and eir1, because in these cases the ARF genes were up-regulated, whereas AUX/IAA7 was down-regulated in eir1. On the other hand, the senescence activated genes SAG12 and SAG13, and those connected to oxidative stress were up-regulated in the wild-type, but down-regulated in aux1. The gene CAB1, connected to photosynthesis, was also down-regulated in the wild-type, but up-regulated in aux1. Gene expression recovered in many cases almost to the initial condition in a time lapse of 24 hours, even though some effect persisted for a longer time. In particular, the state of juvenility of arf2 was extended by irradiation, whereas, in all the other cases, senescence was accelerated. The research indicates that through mutant selection or genetic engineering a true possibility exists of producing organism more suitable for life in space.

Transcriptomic Profile of Arabidopsis Rosette Leaves during the Reproductive Stage after Exposure to Ionizing Radiation

We attempted to obtain a transcriptomic profile of ionizing radiation-responsive genes in Arabidopsis plants using Affymetrix ATH1 whole-genome microarrays. The Arabidopsis plants were irradiated with 200 Gy gamma rays at the early reproduction stage, 33 days after sowing. Rosette leaves were harvested during the postirradiation period from 36 to 49 days after sowing and used for the microarray analysis. The most remarkable changes in the genome-wide expression were observed at 42 days after sowing (9 days after the irradiation). We identified 2165 genes as gamma-ray inducible and 1735 genes as gamma-ray repressible. These numbers of affected genes were almost two to seven times higher than those at other times. In a comparison of the control and irradiated groups, we also identified 354 differentially expressed genes as significant by applying Welch's t test and fold change analysis. The gene ontology analysis showed that radiation up-regulated defense/ stress responses but down-regulated rhythm/growth responses. Specific expression patterns of 10 genes for antioxidant enzymes, photosynthesis or chlorophyll synthesis after irradiation were also obtained using real-time quantitative PCR analysis. We discuss physiological and genetic alterations in the antioxidative defense system, photosynthesis and chlorophyll metabolism after irradiation at the reproductive stage.

Transcriptome analysis reveals fundamental differences in plant response to acute and chronic exposure to ionizing radiation

We analyzed the influence of acute and chronic ionizing radiation (IR) on plant genome stability and global genome expression. Plants from the "chronic" group were grown for 21 days on (137)Cs-artificially contaminated soil, and received a cumulative dose of 1Gy. The "acute" plant group was exposed to an equal dose of radiation delivered as a single pulse. Analysis of homologous recombination (HR) events revealed a significantly higher increase in HR frequency (HRF) in the "chronic" group as compared to "acute" group. To understand the observed difference we performed global genome expression analysis. RNA profiling at 2h and 24h after acute irradiation showed two-third of up- and down-regulated genes to be similarly regulated at both time points. In contrast, less than 10% of the genes up- or down-regulated at 2h or 24h post-acute irradiation were similarly changed after chronic exposure. Promoter analysis revealed substantial differences in the specific regulatory elements found in acute and chronic transcriptomes. Further comparison of the data with existing profiles for several stresses, including UVC and heavy metals, showed substantial transcriptome similarities with the acute but not the chronic transcriptome. Plants exposed to chronic but not acute radiation showed early flowering; transcriptome analysis also revealed induction of flowering genes in "chronic" group.