A DNA-damage-induced cell cycle checkpoint in Arabidopsis

Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types

Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.

Mechanistic insights into DNA damage recognition and checkpoint control in plants

The plant DNA damage response (DDR) pathway safeguards genomic integrity by rapid recognition and repair of DNA lesions that, if unrepaired, may cause genome instability. Most frequently, DNA repair goes hand in hand with a transient cell cycle arrest, which allows cells to repair the DNA lesions before engaging in a mitotic event, but consequently also affects plant growth and yield. Through the identification of DDR proteins and cell cycle regulators that react to DNA double-strand breaks or replication defects, it has become clear that these proteins and regulators form highly interconnected networks. These networks operate at both the transcriptional and post-transcriptional levels and include liquid-liquid phase separation and epigenetic mechanisms. Strikingly, whereas the upstream DDR sensors and signalling components are well conserved across eukaryotes, some of the more downstream effectors are diverged in plants, probably to suit unique lifestyle features. Additionally, DDR components display functional diversity across ancient plant species, dicots and monocots. The observed resistance of DDR mutants towards aluminium toxicity, phosphate limitation and seed ageing indicates that gaining knowledge about the plant DDR may offer solutions to combat the effects of climate change and the associated risk for food security.

Unveiling the structure and interactions of SOG1, a NAC domain transcription factor: An in-silico perspective

SOG1 is a crucial plant-specific NAC domain family transcription factor and functions as the central regulator of DNA damage response, acting downstream of ATM and ATR kinases. In this study, various in-silico approaches have been employed for the characterization of SOG1 transcription factor in a comparative manner with its orthologues from various plant species. Amino acid sequences of more than a hundred SOG1 or SOG1-like proteins were retrieved and their relationship was determined through phylogenetic and motif analyses. Various physiochemical properties and secondary structural components of SOG1 orthologues were determined in selective plant species including Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, and Physcomitrella patens. Furthermore, fold recognition or threading and homology-based three-dimensional models of SOG1 were constructed followed by subsequent evaluation of quality and accuracy of the generated protein models. Finally, extensive DNA-Protein and Protein-Protein interaction studies were performed using the HADDOCK server to give an insight into the mechanism of how SOG1 binds with the promoter region of its target genes or interacts with other proteins to regulate the DNA damage responses in plants. Our docking analysis data have shown the molecular mechanism of SOG1's binding with 5'-CTT(N)7AAG-3' and 5'-(N)4GTCAA(N)4-3' consensus sequences present in the promoter region of its target genes. Moreover, SOG1 physically interacts and forms a thermodynamically stable complex with NAC103 and BRCA1 proteins, which possibly serve as coactivators or mediators in the transcription regulatory network of SOG1. Overall, our in-silico study will provide meaningful information regarding the structural and functional characterization of the SOG1 transcription factor.

Zeocin-induced DNA damage response in barley and its dependence on ATR

DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.

The long non-coding RNA LINDA restrains cellular collapse following DNA damage in Arabidopsis thaliana

The genomic integrity of every organism is endangered by various intrinsic and extrinsic stresses. To maintain genomic integrity, a sophisticated DNA damage response (DDR) network is activated rapidly after DNA damage. Notably, the fundamental DDR mechanisms are conserved in eukaryotes. However, knowledge about many regulatory aspects of the plant DDR is still limited. Important, yet little understood, regulatory factors of the DDR are the long non-coding RNAs (lncRNAs). In humans, 13 lncRNAs functioning in DDR have been characterized to date, whereas no such lncRNAs have been characterized in plants yet. By meta-analysis, we identified the putative long intergenic non-coding RNA induced by DNA damage (LINDA) that responds strongly to various DNA double-strand break-inducing treatments, but not to replication stress induced by mitomycin C. After DNA damage, LINDA is rapidly induced in an ATM- and SOG1-dependent manner. Intriguingly, the transcriptional response of LINDA to DNA damage is similar to that of its flanking hypothetical protein-encoding gene. Phylogenetic analysis of putative Brassicales and Malvales LINDA homologs indicates that LINDA lncRNAs originate from duplication of a flanking small protein-encoding gene followed by pseudogenization. We demonstrate that LINDA is not only needed for the regulation of this flanking gene but also fine-tuning of the DDR after the occurrence of DNA double-strand breaks. Moreover, Δlinda mutant root stem cells are unable to recover from DNA damage, most likely due to hyper-induced cell death.

Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demonstrated to cope with replication defects, accumulating evidence points to other pathways functioning independent of SOG1. Here, we report the roles of the Arabidopsis E2FA and EF2B transcription factors, two well-characterized regulators of DNA replication, in plant response to replication stress. Through a combination of reverse genetics and chromatin immunoprecipitation approaches, we show that E2FA and E2FB share many target genes with SOG1, providing evidence for their involvement in the DDR. Analysis of double- and triple-mutant combinations revealed that E2FB, rather than E2FA, plays the most prominent role in sustaining plant growth in the presence of replication defects, either operating antagonistically or synergistically with SOG1. Conversely, SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants. Collectively, our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.

Translational control of SOG1 expression in response to replication stress in Arabidopsis

DNA damage, which may arise from cellular activities or be induced by genotoxic stresses, can cause genome instability and significantly affect plant growth and productivity. In response to genotoxic stresses, plants activate the cellular DNA damage response (DDR) to sense the stresses and activate downstream processes. The transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a functional counterpart of mammalian p53, is a master regulator of the DDR in plants. It is activated by various types of DNA lesions and can activate the transcription of hundreds of genes to trigger downstream processes, including cell cycle arrest, DNA repair, endoreplication, and apoptosis. Since SOG1 plays a crucial role in DDR, the activity of SOG1 must be tightly regulated. A recent study published in Plant Cell (Chen et al., Plant Cell koad126, 2023) reports a novel mechanism by which the ATR-WEE1 kinase module promotes SOG1 translation to fine-tune replication stress response.

Integrative Transcriptomics Data Mining to Explore the Functions of TDP1α and TDP1β Genes in the Arabidopsis thaliana Model Plant

The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA in the DNA-topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α has been linked to genome stability maintenance, while TDP1β has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1β seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1α is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles.

Physiological and biochemical markers of gamma irradiated white radish (Raphanus sativus)

PURPOSE

A field experiment was performed to investigate the impact of low-dose gamma rays on growth parameters and bioactive compounds of white radish.

MATERIALS AND METHODS

White radish seeds were irradiated by gamma rays dose levels (10, 20, 40 and 80 Gy) beside control. Physiological and biochemical markers were done to follow the effect of gamma rays on white radish.

RESULTS

The results revealed that gamma rays increased growth parameters with increasing irradiation to a dose of 40 Gy. The maximum increments were found at 14.64 (cm), 48.30 (cm), 20.84 (cm) and 5.51 (cm) for leaves number, leaves length, roots length and roots diameter, respectively, with a dose of 40 Gy. By increasing the irradiation dose to 80 Gy, the results showed reduction in all parameters studied. Ascorbic acid gave the maximum increase with the dose of 40 Gy, while phenols, flavonoids, antioxidant activity, peroxidase, and polyphenol oxidase showed the highest increase with the dose 80 of Gy in radish leaves. Similar trend was observed for the radish roots. Furthermore, the protein and isoenzyme profiles of peroxidase and polyphenol oxidase changed and induced alteration by different irradiation dose levels.

CONCLUSION

Gamma rays can be a useful tool for increasing the growth and biochemical content of white radish plants and perhaps other food crops.

How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants

DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.

Analysis of BRCT5 domain-containing proteins reveals a new component of DNA damage repair in Arabidopsis

The integrity of plant genetic information is constantly challenged by various internal and external factors. Therefore, plants use a sophisticated molecular network to identify, signal and repair damaged DNA. Here, we report on the identification and analysis of four uncharacterized Arabidopsis BRCT5 DOMAIN CONTAINING PROTEINs (BCPs). Proteins with the BRCT5 domain are frequently involved in the maintenance of genome stability across eukaryotes. The screening for sensitivity to induced DNA damage identified BCP1 as the most interesting candidate. We show that BCP1 loss of function mutants are hypersensitive to various types of DNA damage and accumulate an increased number of dead cells in root apical meristems upon DNA damage. Analysis of publicly available sog1 transcriptomic and SOG1 genome-wide DNA binding data revealed that BCP1 is inducible by gamma radiation and is a direct target of this key DNA damage signaling transcription factor. Importantly, bcp1 plants showed a reduced frequency of somatic homologous recombination in response to both endogenous and induced DNA damage. Altogether, we identified a novel plant-specific DNA repair factor that acts downstream of SOG1 in homology-based repair.

Gamma Radiation Induced In-Vitro Mutagenesis and Isolation of Mutants for Early Flowering and Phytomorphological Variations in Dendrobium 'Emma White'

In vitro mutagenesis offers a feasible approach for developing new orchid cultivars through genetic manipulation. In the present study, protocorm-like bodies (PLBs) were exposed to gamma rays (10, 20, 40, 60, 80 Gy) to study in vitro growth responses and induction of mutants in Dendrobium ‘Emma White’. Both proliferation and regeneration of PLBs decreased progressively with increasing doses, except for a significantly enhanced growth response at 10 Gy. The optimal dose of gamma radiation for mutagenesis was found in the range 10 to 25 Gy based on the growth reduction curve. Analysis using a high-throughput cell analyzer revealed a significant reduction in nuclear DNA content at > 40 Gy doses. At 10 Gy treatment, the growth attributes, such as root length, plant height and leaf number, were significantly increased by 36%, 26% and 20%, respectively, compared to the control. This increase was significant over other tested doses as well. Testing of random amplified polymorphic DNA markers revealed the presence of detectable polymorphism among gamma mutant plantlets with a polymorphism information content value at 0.41. The gamma-ray-induced earliness in flower development was observed within 294 days post ex vitro growth of 10 Gy mutant compared to the control plants flowered after 959 days. Our results highlight the significance of gamma radiation in inducing enhanced growth, morphological variations and early floral initiation in Dendrobium, providing a basic framework for mutation breeding and improvement of orchids.

Application of gamma irradiation on morphological, biochemical, and molecular aspects of wheat (Triticum aestivum L.) under different seed moisture contents

Nuclear technology is currently used as a tool in mutation breeding to improve crops by increasing genetic variation. The ionization of gamma rays produces large amounts of free radicals, simulating stressors in the natural environment. To avoid gamma-ray-induced oxidative stress, plants use antioxidant defense systems. Exposure of plants to irradiation can affect the germination, growth, and production of metabolites. Plants' sensitivity to irradiation depends on genetic and environmental factors such as moisture content. For this purpose, the effects of different gamma irradiation doses [0, 100, 200, 300, and 400 Gray (Gy)] and different seed moisture contents (7, 13, and 19%) on traits such as seed germination, seedling growth, molecular and biochemical alterations in antioxidant enzymes were examined in the current study. Based on the results, the highest seed germination percentage was observed in the interaction effect of seed moisture at 13% with an irradiation dose of 400 Gy (98.89%). Seedling survival percent and seedling length decreased with increasing doses of gamma irradiation at different seed moisture contents. Increasing gamma irradiation doses were reduced root and stem fresh and dry weight, and root and stem length. The highest level of catalase enzyme activity and expression was observed at 200 and 300 Gy irradiation doses at different moisture contents. The peroxidase and polyphenol oxidase gene expression were reduced at all contents of gamma irradiation doses and seed moisture compared to the control. It can be concluded that the dose of 200-300 Gy of gamma irradiation reduced plant growth by 30% in terms of fresh and dry weight and length of plants, as well as enhanced the expression of antioxidant enzymes. The results of this study could help plant breeders select an appropriate dose rate in wheat for further research.

Effects of gamma irradiation on morphology and protein differential in M1V1 population of Vanilla planifolia Andrews

PURPOSE

Lower doses (1-10 Krad) of gamma-rays (γ) are frequently used in obtaining useful mutants in diverse plant species, whereas no report on gamma (γ) irradiation being used to develop new varieties of vanilla from vanilla cuttings. This study assessed the potential of lower doses of gamma-rays for vanilla mutation breeding.

MATERIALS AND METHODS

We compared the morphological differences between vanilla plants irradiated at different lower doses of gamma radiation (10, 30, 40, and 50 Gy). We quantified protein and compared variation from the extracted protein of vanilla shoots regenerated between treatments.

RESULTS AND CONCLUSIONS

After 44 weeks, the results showed that the growth of M1V1 (mutation 1 in vegetative cycle 1) plants at 0 Gy (control) is highest compared with other doses of gamma radiation in terms of plant height and the number of shoots. However, the highest measurement for root length is at 10 Gy. The slowest growth rate was obtained from 40 to 50 Gy. Based on the unique band of protein that appears on the SDS-PAGE gel, 10 Gy has three unique bands at loci 0.105 RF, two bands lie at loci between 0.164 RF and 0.234 RF. While 30 Gy is absent two unique bands at loci 0.234 RF compared to 0 Gy. Thus, the dose of gamma rays at 10 Gy gave the highest number of protein fragments, which detected polymorphisms between the control (0 Gy) and the plants treated. To our knowledge, this is the first report of the protein variation in M1V1 of irradiated vanilla plants.

Identification and Characterization of SOG1 (Suppressor of Gamma-Response 1) Homologues in Plants Using Data Mining Resources and Gene Expression Profiling

SOG1 (Suppressor of the Gamma response 1) is the master-regulator of plant DNA damage response (DDR), a highly coordinated network of DNA damage sensors, transducers, mediators, and effectors, with highly coordinated activities. SOG1 transcription factor belongs to the NAC/NAM protein family, containing the well-conserved NAC domain and five serine-glutamine (SQ) motifs, preferential targets for phosphorylation by ATM and ATR. So far, the information gathered for the SOG1 function comes from studies on the model plant Arabidopsis thaliana. To expand the knowledge on plant-specific DDR, it is opportune to gather information on other SOG1 orthologues. The current study identified plants where multiple SOG1 homologues are present and evaluated their functions by leveraging the information contained in publicly available transcriptomics databases. This analysis revealed the presence of multiple SOG1 sequences in thirteen plant species, and four (Medicago truncatula, Glycine max, Kalankoe fedtschenkoi, Populus trichocarpa) were selected for gene expression data mining based on database availability. Additionally, M. truncatula seeds and seedlings exposed to treatments known to activate DDR pathways were used to evaluate the expression profiles of MtSOG1a and MtSOG1b. The experimental workflow confirmed the data retrieved from transcriptomics datasets, suggesting that the SOG1 homologues have redundant functions in different plant species.

Biological Effect of Gamma Rays According to Exposure Time on Germination and Plant Growth in Wheat

Gamma rays as a type of ionizing radiation constitute a physical mutagen that induces mutations and could be effectively used in plant breeding. To compare the effects of gamma and ionizing irradiation according to exposure time in common wheat (Keumgang, IT 213100), seeds were exposed to 60Co gamma rays at different dose rates. To evaluate the amount of free radical content, we used electron spin resonance spectroscopy. Significantly more free radicals were generated in the case of long-term compared with short-term gamma-ray exposure at the same dose of radiation. Under short-term exposure, shoot and root lengths were slightly reduced compared with those of the controls, whereas long-term exposure caused severe growth inhibition. The expression of antioxidant-related and DNA-repair-related genes was significantly decreased under long-term gamma-ray exposure. Long-term exposure caused higher radiosensitivity than short-term exposure. The results of this study could help plant breeders select an effective mutagenic induction dose rate in wheat.

Gamma rays induced genetic variability in tomato (Solanum lycopersicum L.) germplasm

The present study assessed the effectiveness of gamma radiation in inducing favorable genetic variability in tomato (Solanum lycopersicum L.). An experiment was conducted in a randomized complete block design to produce M₁ generation. Significant differences were observed among the genotypes as well as between the treatments at individual plant level based on observed traits (seed germination percentage, seedling survival, plant height, number of flower clusters plant⁻¹, number of flowers and fruits plant⁻¹). All observed characters in the mutagenized population were adversely affected with increasing radiation dose. Results identified 450 Gy as the most damaging radiation dose followed by 300 Gy and 150 Gy. Moreover, 300 Gy treatment was identified as lethal dose (LD₅₀) as it caused a 50% germination inhibition in almost all the evaluated genotypes. The 150 Gy treatment showed the least damaging impact and induced maximum genetic variability in almost all the genotypes under study. Character association studies were also conducted which could be utilized in the selection of desirable mutants. Correlation studies revealed an altered association among the observed parameters from positive to negative direction in 300 Gy and 450 Gy treatments as compared to control. These deviations in correlation coefficients proved that mutagenesis can break the linkage among specific loci. Furthermore, path coefficient analysis identified the growth attributes with an effective direct and indirect contribution in yield.

Cell cycle checkpoint control in response to DNA damage by environmental stresses

Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.

Gamma irradiation to induce beneficial mutants in proso millet (Panicum miliaceum L.): an underutilized food crop

PURPOSE

Proso millet is a potential crop for food, nutritional security, and sustainable agriculture, particularly in the context of climate change. It is one of the traditional millet crops in cultivation in Tamil Nadu and India. Self-pollinated nature of this crop makes evolutionary process a terminal one and creating variability to broaden the genetic base is important. The objective of the study was to optimize mutagenic dose of gamma mutagen, document types of mutations and identify mutants for high grain yield (GY) and fodder yield (FY), hence to determine the feasibility of gamma mutagenesis in proso millet crop improvement.

MATERIALS AND METHODS

A mutation breeding program with 10 doses of gamma irradiation, i.e. 100, 200, 300, 400, 500, 600, 700, 800, 900 and 1000 Gy were imposed on seeds of variety ATL 1, a popular variety in India. Roll paper method, tray method and field evaluation were carried out to determine the LD₅₀ and GR₅₀ doses. Based on viable mutation frequency in M₂ generation, mutagenic effectiveness and efficiency was estimated. Targeted selection for yield and yield contributing traits was carried out in M₂, M₃ and M₄ generation to identify high yielding mutants.

RESULTS

The LD₅₀ and GR₅₀ doses of gamma were estimated to be 418 Gy and 542 Gy, respectively. Based on results from probit analysis, mutagenic effectiveness, mutagenic efficiency and mutation spectrum, the optimum treatment dose of gamma was concluded to be 400 Gy. High frequency, i.e. 10.96% of phenotypic mutants was identified in the M₂ generation. The broad range of mutants identified in M₂ generation had mutations for plant height, plant habit, panicle shape, compactness, and length, days to 50% flowering (DFF), lodging resistance, tillering, leaf phenotype, apiculus color, culm branching, stem and leaf hairiness, sheath pigmentation, seed color and shape and seed coat attachment. Eight high yielding mutant families were isolated in M₄ generation. The mean single plant GY and FY of these mutants ranged between 25 to 51 g and 40 to 68 g respectively while in control it was 15 g and 30 g, respectively.

CONCLUSIONS

The wide spectrum and high frequency of mutations both for qualitative and quantitative traits suggest mutation induction as a promising method for creating novel variations in proso millet. The high yielding mutants identified can be utilized for varietal development both for grain and fodder purpose after further stability and quality evaluations in the advanced generations.

SOG1, a plant-specific master regulator of DNA damage responses, originated from nonvascular land plants

The suppressor of gamma response 1 (SOG1), a NAM, ATAF1, 2, and CUC2 (NAC)-type transcription factor found in seed plants, is a master regulator of DNA damage responses (DDRs). Upon DNA damage, SOG1 regulates the expression of downstream DDR genes. To know the origin of the DDR network in land plants, we searched for a homolog(s) of SOG1 in a moss Physcomitrium (Physcomitrella) patens and identified PpSOG1a and PpSOG1b. To assess if either or both of them function(s) in DDR, we knocked out the PpSOG1s using CRISPR/Cas9-mediated gene editing and analyzed the responses to DNA-damaging treatments. The double-knockout (KO) sog1a sog1b plants showed resistance to γ-rays, bleomycin, and ultraviolet B (UVB) treatments similarly seen in Arabidopsis sog1 plants. Next, we irradiated wild-type (WT) and KO plants with γ-rays and analyzed the whole transcriptome to examine the effect on the expression of DDR genes. The results revealed that many P. patens genes involved in the checkpoint, DNA repair, replication, and cell cycle-related genes were upregulated after γ-irradiation, which was not seen in sog1a sog1b plant. These results suggest that PpSOG1a and PpSOG1b work redundantly on DDR response in P. patens; in addition, plant-specific DDR systems had been established before the emergence of vascular plants.

DNA Damage Responses during the Cell Cycle: Insights from Model Organisms and Beyond

Genome damage is a threat to all organisms. To respond to such damage, DNA damage responses (DDRs) lead to cell cycle arrest, DNA repair, and cell death. Many DDR components are highly conserved, whereas others have adapted to specific organismal needs. Immense progress in this field has been driven by model genetic organism research. This review has two main purposes. First, we provide a survey of model organism-based efforts to study DDRs. Second, we highlight how model organism study has contributed to understanding how specific DDRs are influenced by cell cycle stage. We also look forward, with a discussion of how future study can be expanded beyond typical model genetic organisms to further illuminate how the genome is protected.

XAP5 CIRCADIAN TIMEKEEPER Affects Both DNA Damage Responses and Immune Signaling in Arabidopsis

Numerous links have been reported between immune response and DNA damage repair pathways in both plants and animals but the precise nature of the relationship between these fundamental processes is not entirely clear. Here, we report that XAP5 CIRCADIAN TIMEKEEPER (XCT), a protein highly conserved across eukaryotes, acts as a negative regulator of immunity in Arabidopsis thaliana and plays a positive role in responses to DNA damaging radiation. We find xct mutants have enhanced resistance to infection by a virulent bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, and are hyper-responsive to the defense-activating hormone salicylic acid (SA) when compared to wild-type. Unlike most mutants with constitutive effector-triggered immunity (ETI), xct plants do not have increased levels of SA and retain enhanced immunity at elevated temperatures. Genetic analysis indicates XCT acts independently of NONEXPRESSOR OF PATHOGENESIS RELATED GENES1 (NPR1), which encodes a known SA receptor. Since DNA damage has been reported to potentiate immune responses, we next investigated the DNA damage response in our mutants. We found xct seedlings to be hypersensitive to UV-C and γ radiation and deficient in phosphorylation of the histone variant H2A.X, one of the earliest known responses to DNA damage. These data demonstrate that loss of XCT causes a defect in an early step of the DNA damage response pathway. Together, our data suggest that alterations in DNA damage response pathways may underlie the enhanced immunity seen in xct mutants.

Connections between the Cell Cycle and the DNA Damage Response in Plants

Due to their sessile lifestyle, plants are especially exposed to various stresses, including genotoxic stress, which results in altered genome integrity. Upon the detection of DNA damage, distinct cellular responses lead to cell cycle arrest and the induction of DNA repair mechanisms. Interestingly, it has been shown that some cell cycle regulators are not only required for meristem activity and plant development but are also key to cope with the occurrence of DNA lesions. In this review, we first summarize some important regulatory steps of the plant cell cycle and present a brief overview of the DNA damage response (DDR) mechanisms. Then, the role played by some cell cycle regulators at the interface between the cell cycle and DNA damage responses is discussed more specifically.

SOG1 transcription factor promotes the onset of endoreduplication under salinity stress in Arabidopsis

As like in mammalian system, the DNA damage responsive cell cycle checkpoint functions play crucial role for maintenance of genome stability in plants through repairing of damages in DNA and induction of programmed cell death or endoreduplication by extensive regulation of progression of cell cycle. ATM and ATR (ATAXIA-TELANGIECTASIA-MUTATED and -RAD3-RELATED) function as sensor kinases and play key role in the transmission of DNA damage signals to the downstream components of cell cycle regulatory network. The plant-specific NAC domain family transcription factor SOG1 (SUPPRESSOR OF GAMMA RESPONSE 1) plays crucial role in transducing signals from both ATM and ATR in presence of double strand breaks (DSBs) in the genome and found to play crucial role in the regulation of key genes involved in cell cycle progression, DNA damage repair, endoreduplication and programmed cell death. Here we report that Arabidopsis exposed to high salinity shows generation of oxidative stress induced DSBs along with the concomitant induction of endoreduplication, displaying increased cell size and DNA ploidy level without any change in chromosome number. These responses were significantly prominent in SOG1 overexpression line than wild-type Arabidopsis, while sog1 mutant lines showed much compromised induction of endoreduplication under salinity stress. We have found that both ATM-SOG1 and ATR-SOG1 pathways are involved in the salinity mediated induction of endoreduplication. SOG1was found to promote G2-M phase arrest in Arabidopsis under salinity stress by downregulating the expression of the key cell cycle regulators, including CDKB1;1, CDKB2;1, and CYCB1;1, while upregulating the expression of WEE1 kinase, CCS52A and E2Fa, which act as important regulators for induction of endoreduplication. Our results suggest that Arabidopsis undergoes endoreduplicative cycle in response to salinity induced DSBs, showcasing an adaptive response in plants under salinity stress.

Gamma radiation negatively impacted seed germination, seedling growth and antioxidant enzymes activities in tall fescue infected with Epichloë endophyte

Plants and their accompanying microorganisms growing in contaminated sites with long-lived gamma-emitting radionuclides may be affected by radiation stress. The present study aimed to investigate the effects of gamma radiation on symbiotic relationship between Epichloë endophyte and Festuca arundinacea plant along with the radio-sensitivity of a pair of clones of tall fescue with (E+) and without (E-) symbiotic Epichloë endophyte exposed to different doses of gamma radiation including 25, 50, 75, 100, 150, 200, 300, and 400 Gray (Gy) from a Cobalt-60 source. Both irradiated and non-irradiated seeds of each status were grown under controlled conditions. Seed germination indices, seedling growth and certain physiological criteria associated with plant responses to oxidative stress were examined. The results revealed that low doses (up to 75 Gy) of gamma radiation stimulated seed germination indices and seedling growth. However, high doses (100-400 Gy) significantly reduced the final germination percentage, germination rate index, coefficient of velocity of germination, and the seed reserve depletion percentage, and enhanced the mean germination time. Further, high doses of radiation reduced root and shoot lengths, root and shoot fresh weights, and activities of antioxidant enzymes (especially catalase and superoxide dismutase), and increased the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) of the seedlings. The results showed that the endophyte was present in seeds after gamma ray irradiation. However, the presence of endophyte in seedlings started to be reduced significantly (18.45% reduction rather than the control) at 50 Gy of gamma radiation. High doses (100 Gy and above) dramatically declined the presence of endophyte down to zero in seedlings compared to the control. In this study, the E- clone had higher seed germination and seedling growth as well as lower H2O2 and MDA contents under radiation stress as compared with the E+ clone. Additionally, shoot tolerance index (STI) indicated more radiation tolerance in the E- clone. According to the results of the present study, it is concluded that biological impacts of gamma radiation stress and the harmful effects on endophyte viability may cause more radio-sensitivity and changes in the growth and physio-biochemical aspects of the host plant.

Plant cell cycle regulators: Mitogen-activated protein kinase, a new regulating switch?

Cell cycle is essential for the maintenance of genetic material and continuity of a species. Its regulation involves a complex interplay between multiple proteins with diverse molecular functions such as the kinases, transcription factors, proteases and phosphatases. Every step of this cycle requires a certain combination of these protein regulators which paves the way for the next stage. It is now evident that plants have their own unique features in the context of cell cycle regulation. Cell cycle in plants is not only necessary for maintenance of its physio-morphological parameter but it also regulates traits important for mankind like grain or fruit size. This makes it even more important to understand how plants regulate its cell cycle amidst various a/biotic stresses it is subjected to during its lifetime. The association of MAPK signaling pathways with every major developmental and stress response pathways in plants raises the question of its potential role in cell cycle regulation. There are number of cell cycle regulating proteins with putative sites for MAPK phosphorylation. The MAPK signaling pathway may directly or in a parallel pathway regulate the plant cell cycle. Unraveling the role of MAPK in cell cycle will open up new arenas to explore.

Technical note: Gamma irradiation induces changes of phenotypic and agronomic traits in wheat (Triticum turgidum ssp. durum)

WHEAT VAR

CIRNO C2008 was irradiated with gamma rays at 100, 200, and 300 Gy. The irradiated plants obtained at 300 Gy (M₁) showed a significant reduction (compared to M₀ plants) in germination (i.e. 3.8% at day 5), survival percentage (48%), and plant height (63.3%). Thus, the Probit analysis showed an LD₅₀ of 287.80 Gy. Besides, these irradiated plants, in the field, showed a significant increase (compared to M₀ plants) in days to spike initiation (16 days), and maturation (14 days). On the other hand, in the field, fourteen chlorophyll mutants were found (at a different frequency) in the M₂ generation, such as Albina, Anthocyanin, Chlorina, Maculata, Tigrina, Striata, Viridis, Viridoalbina, Alboviridis, Xantha, Xanthviridis, Xanthalba, Viridoxantha, and Orange stem. In addition, mutants with changes in agronomic and morphological traits were observed. This nuclear technique is an alternative to obtain promising mutant lines that can be used directly as a variety and/or as parental to transfer these traits to other varieties.

FATTY ACID DESATURASE5 Is Required to Induce Autoimmune Responses in Gigantic Chloroplast Mutants of Arabidopsis

Chloroplasts mediate genetically controlled cell death via chloroplast-to-nucleus retrograde signaling. To decipher the mechanism, we examined chloroplast-linked lesion-mimic mutants of Arabidopsis (Arabidopsis thaliana) deficient in plastid division, thereby developing gigantic chloroplasts (GCs). These GC mutants, including crumpled leaf (crl), constitutively express immune-related genes and show light-dependent localized cell death (LCD), mirroring typical autoimmune responses. Our reverse genetic approach excludes any potential role of immune/stress hormones in triggering LCD. Instead, transcriptome and in silico analyses suggest that reactive electrophile species (RES) generated via oxidation of polyunsaturated fatty acids (PUFAs) or lipid peroxidation-driven signaling may induce LCD. Consistent with these results, the one of the suppressors of crl, dubbed spcrl4, contains a causative mutation in the nuclear gene encoding chloroplast-localized FATTY ACID DESATURASE5 (FAD5) that catalyzes the conversion of palmitic acid (16:0) to palmitoleic acid (16:1). The loss of FAD5 in the crl mutant might attenuate the levels of RES and/or lipid peroxidation due to the reduced levels of palmitic acid-driven PUFAs, which are prime targets of reactive oxygen species. The fact that fad5 also compromises the expression of immune-related genes and the development of LCD in other GC mutants substantiates the presence of an intrinsic retrograde signaling pathway, priming the autoimmune responses in a FAD5-dependent manner.

Adaptation to ionizing radiation of higher plants: From environmental radioactivity to chernobyl disaster

The purpose of this work is to highlight the effects of ionizing radiation on the genetic material in higher plants by assessing both adaptive processes as well as the evolution of plant species. The effects that the ionizing radiation has on greenery following a nuclear accident, was examined by taking the Chernobyl Nuclear Power Plant disaster as a case study. The genetic and evolutionary effects that ionizing radiation had on plants after the Chernobyl accident were highlighted. The response of biota to Chernobyl irradiation was a complex interaction among radiation dose, dose rate, temporal and spatial variation, varying radiation sensitivities of the different plants' species, and indirect effects from other events. Ionizing radiation causes water radiolysis, generating highly reactive oxygen species (ROS). ROS induce the rapid activation of detoxifying enzymes. DeoxyriboNucleic Acid (DNA) is the object of an attack by both, the hydroxyl ions and the radiation itself, thus triggering a mechanism both direct and indirect. The effects on DNA are harmful to the organism and the long-term development of the species. Dose-dependent aberrations in chromosomes are often observed after irradiation. Although multiple DNA repair mechanisms exist, double-strand breaks (DSBs or DNA-DSBs) are often subject to errors. Plants DSBs repair mechanisms mainly involve homologous and non-homologous dependent systems, the latter especially causing a loss of genetic information. Repeated ionizing radiation (acute or chronic) ensures that plants adapt, demonstrating radioresistance. An adaptive response has been suggested for this phenomenon. As a result, ionizing radiation influences the genetic structure, especially during chronic irradiation, reducing genetic variability. This reduction may be associated with the fact that particular plant species are more subject to chronic stress, confirming the adaptive theory. Therefore, the genomic effects of ionizing radiation demonstrate their likely involvement in the evolution of plant species.

The F-Box-Like Protein FBL17 Is a Regulator of DNA-Damage Response and Colocalizes with RETINOBLASTOMA RELATED1 at DNA Lesion Sites

In Arabidopsis (Arabidopsis thaliana), the F-box protein F-BOX-LIKE17 (FBL17) was previously identified as an important cell-cycle regulatory protein. FBL17 is required for cell division during pollen development and for normal cell-cycle progression and endoreplication during the diploid sporophyte phase. FBL17 was reported to control the stability of the CYCLIN-DEPENDENT KINASE inhibitor KIP-RELATED PROTEIN (KRP), which may underlie the drastic reduction in cell division activity in both shoot and root apical meristems observed in fbl17 loss-of-function mutants. However, whether FBL17 has other substrates and functions besides degrading KRPs remains poorly understood. Here we show that mutation of FBL17 leads not only to misregulation of cell cycle genes, but also to a strong upregulation of genes involved in DNA damage and repair processes. This phenotype is associated with a higher frequency of DNA lesions in fbl17 and increased cell death in the root meristem, even in the absence of genotoxic stress. Notably, the constitutive activation of DNA damage response genes is largely SOG1-independent in fbl17 In addition, through analyses of root elongation, accumulation of cell death, and occurrence of γH2AX foci, we found that fbl17 mutants are hypersensitive to DNA double-strand break-induced genotoxic stress. Notably, we observed that the FBL17 protein is recruited at nuclear foci upon double-strand break induction and colocalizes with γH2AX, but only in the presence of RETINOBLASTOMA RELATED1. Altogether, our results highlight a role for FBL17 in DNA damage response, likely by ubiquitylating proteins involved in DNA-damage signaling or repair.

High-Throughput Phenotyping (HTP) Data Reveal Dosage Effect at Growth Stages in Arabidopsis thaliana Irradiated by Gamma Rays

The effects of radiation dosages on plant species are quantitatively presented as the lethal dose or the dose required for growth reduction in mutation breeding. However, lethal dose and growth reduction fail to provide dynamic growth behavior information such as growth rate after irradiation. Irradiated seeds of Arabidopsis were grown in an environmentally controlled high-throughput phenotyping (HTP) platform to capture growth images that were analyzed with machine learning algorithms. Analysis of digital phenotyping data revealed unique growth patterns following treatments below LD50 value at 641 Gy. Plants treated with 100-Gy gamma irradiation showed almost identical growth pattern compared with wild type; the hormesis effect was observed >21 days after sowing. In 200 Gy-treated plants, a uniform growth pattern but smaller rosette areas than the wild type were seen (p < 0.05). The shift between vegetative and reproductive stages was not retarded by irradiation at 200 and 300 Gy although growth inhibition was detected under the same irradiation dose. Results were validated using 200 and 300 Gy doses with HTP in a separate study. To our knowledge, this is the first study to apply a HTP platform to measure and analyze the dosage effect of radiation in plants. The method enabled an in-depth analysis of growth patterns, which could not be detected previously due to a lack of time-series data. This information will improve our knowledge about the effects of radiation in model plant species and crops.

Alternative Splicing and DNA Damage Response in Plants

Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.

Physiological consequences of gamma ray irradiation in tall fescue with elimination potential of Epichloë fungal endophyte

Perennial plants and their associated microorganisms grow in the areas that may be contaminated with long-lived gamma-emitting radionuclides. This will induce gamma stress response in plants and their accompanying microorganisms. The present work investigated the growth and physiological responses of Epichloe endophyte infected tall fescue to gamma radiation, as well as whether the endophyte could persist and infect the host plant once exposed to gamma radiation. Seeds of Iranian native genotype of 75B⁺ of tall fescue were exposed to different doses, including 5.0, 10.0, 15.0, 20.0, 30.0 and 40.0 krad of gamma ray from a ⁶⁰Co source. Irradiated and unirradiated seeds were sown in pots and grown under controlled conditions in the greenhouse. The growth and physiological parameters associated with plant tolerance to oxidative stress of host plants, as well as endophytic infection frequency (% of plants infected) and intensity (mean number of endophytic hyphae per the field of view), were examined in 3 months-old seedlings. The results indicated that all gamma radiation doses (except 5.0 kr) significantly reduced the height and survival percentage of the host plant. Days to the emergence of seedling increased gradually as gamma doses rose. A dose-rate dependent induction was seen for photosynthetic pigments and proline content. Malondialdehyde (MDA) content grew with elevation of irradiation doses. Depending on the dose and time, the activities of antioxidant enzymes in the host plant responded differently to gamma radiation. Gamma radiation altered the enzyme activities with sever decline in SOD and CAT activities. However, it had barely any effect on in APX and POD activities. The results also revealed that the persistence and intensity of endophyte were affected after gamma-ray irradiation. The initial percentage of tall fescue seeds infected with the endophyte was 91% in un-irradiated seeds. Presence of the viable endophyte started to decline significantly (23%) at 5.0 kr of gamma radiation. A dramatic reduction in the presence and intensity of endophyte occurred at 10.0 to 40.0 kr intensities. Gamma radiation × trait (GT)-biplot analysis indicated positive correlations between the endophyte symbiosis and antioxidant enzyme activities. Also, negative correlations were observed between the endophyte and MDA content in the host plant. Our results suggest that radiation stress (doses over 5.0 kr) caused reduction in the growth and antioxidant enzyme activities of the host plant that accompanied by a dramatic reduction in the persistence and intensity of endophyte fungi. Our findings have provided the basic information for future studies on the effect of gamma irradiation on the interaction between endophytic fungi and its host plant.

Gap 2 phase: making the fundamental decision to divide or not

The Gap phases of the cell cycle are essential to perceive internal and external signals and control cell division and differentiation. However, our knowledge of molecular mechanisms underlying G2 progression in plants remains quite limited. In this review, we summarize recent findings about core G2-phase regulators, such as B-type cyclin-dependent kinases (CDKs) and R1R2R3-type MYB transcription factors. We highlight developmental and stress signals that regulate expression and accumulation of the G2-phase regulators, and discuss how they fine-tune mitotic CDK activity and control cell proliferation, endoreplication and cell cycle checkpoints. A particular focus is on DNA damage-induced G2 arrest, which is prerequisite for maintenance of genome stability.

Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens

Telomeres and ribosomal RNA genes (rDNA) are essential for cell survival and particularly sensitive to factors affecting genome stability. Here, we examine the role of RAD51 and its antagonist, RTEL1, in the moss Physcomitrella patens. In corresponding mutants, we analyse their sensitivity to DNA damage, the maintenance of telomeres and rDNA, and repair of double-stranded breaks (DSBs) induced by genotoxins with various modes of action. While the loss of RTEL1 results in rapid telomere shortening, concurrent loss of both RAD51 genes has no effect on telomere lengths. We further demonstrate here the linked arrangement of 5S and 45S rRNA genes in P. patens. The spacer between 5S and 18S rRNA genes, especially the region downstream from the transcription start site, shows conspicuous clustering of sites with a high propensity to form quadruplex (G4) structures. Copy numbers of 5S and 18S rDNA are reduced moderately in the pprtel1 mutant, and significantly in the double pprad51-1-2 mutant, with no progression during subsequent cultivation. While reductions in 45S rDNA copy numbers observed in pprtel1 and pprad51-1-2 plants apply also to 5S rDNA, changes in transcript levels are different for 45S and 5S rRNA, indicating their independent transcription by RNA polymerase I and III, respectively. The loss of SOL (Sog One-Like), a transcription factor regulating numerous genes involved in DSB repair, increases the rate of DSB repair in dividing as well as differentiated tissue, and through deactivation of G2/M cell-cycle checkpoint allows the cell-cycle progression manifested as a phenotype resistant to bleomycin.

Joint effects of gamma radiation and cadmium on subcellular-, individual- and population-level endpoints of the green microalga Raphidocelis subcapitata

Interpreting and predicting the combined effects of toxicants in the environment is an important challenge in ecotoxicology. How such effects are connected across different levels of biological organisation is an additional matter of uncertainty. Such knowledge gaps are particularly prominent with regards to how ionising radiation interacts with contaminants. We assessed the response of twelve endpoints at the subcellular, individual and population level in a green microalga when exposed singly and jointly to gamma radiation and cadmium (Cd). We used a fully factorial experimental design where observed effects were compared to those predicted by the Independent Action (IA) model for mixture toxicity to determine whether they deviated from additivity. Subcellular endpoints (e.g., catalase, thiamine diphosphate, xanthophyll cycle pigments) showed an increased antioxidant and/or photoprotective response. However, our results indicate that this protection was not sufficient to prevent lipid peroxidation, which also increased with dose. At ecologically relevant doses, most interactions between gamma radiation and Cd regarding subcellular-, individual- and population-level endpoints were additive as predicted by the IA model. However, exposure to binary mixtures displayed antagonistic interactions between gamma radiation and Cd at the higher end of the tested dose spectrum. No correlations were observed between subcellular endpoints and higher-level endpoints, but there were linkages between individual and population endpoints. Our results suggest that antagonistic interactions between gamma radiation and Cd can occur at higher doses and that these interactions seem to disseminate from subcellular and individual to population level. Possible consequences for aquatic primary production and food-web interactions are discussed.

The XPF-ERCC1 Complex Is Essential for Genome Stability and Is Involved in the Mechanism of Gene Targeting in Physcomitrella patens

The XPF-ERCC1 complex, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair, and homologous recombination. XPF-ERCC1 incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here, we have examined the role of the XPF-ERCC1 complex in the model bryophyte Physcomitrella patens which exhibits uniquely high gene targeting frequencies. We undertook targeted knockout of the Physcomitrella ERCC1 and XPF genes. Mutant analysis shows that the endonuclease complex is essential for resistance to UV-B and to the alkylating agent MMS, and contributes to the maintenance of genome integrity but is also involved in gene targeting in this model plant. Using different constructs we determine whether the function of the XPF-ERCC1 endonuclease complex in gene targeting was removal of 3' non-homologous termini, similar to SSA, or processing of looped-out heteroduplex intermediates. Interestingly, our data suggest a role of the endonuclease in both pathways and have implications for the mechanism of targeted gene replacement in plants and its specificities compared to yeast and mammalian cells.

Gamma irradiation induced effects on in vitro shoot cultures and influence of monochromatic light regimes on irradiated shoot cultures of Dendrobium sonia orchid

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Monochromatic light source affected growth of gamma irradiated in vitro cultures of Dendrobium

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Yellow and red monochromatic lights significantly improved survival rate and growth of irradiated cultures.

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Intra-somatic competition among mutated and non-mutated cultures can be managed by monochromatic light through better growth in vitro.

The effects of gamma radiation and monochromatic lights on growth of in vitro shoot cultures of orchid, Dendrobium sonia, were investigated. The gamma irradiated shoot cultures grown under white, blue, yellow and red monochromatic lights exhibited differential growth pattern. Shoot cultures gamma irradiated at 15–45 Gy showed reduced shoot length, fresh weight and leaf area. The monochromatic light significantly influenced survival rate and growth of irradiated shoots. The yellow and red light treatments positively influenced survival of gamma irradiated shoots with significant increase in fresh weight, shoot length and chlorophyll content. Yellow light was found to be most effective as leaf area was increased across the radiation dose range (15–100 Gy) compared to red light. The results demonstrated that the method of post-irradiation exposure could be useful to improve growth of gamma irradiated in vitro shoots, and help to recover orchid mutants with novel modifications.

Efecto de diferentes explantes irradiados en la regeneración <i>in vitro</i> de frijol común <i>(Phaseolus vulgaris </i>L.) cultivar “ICA Pijao”

El mejoramiento genético convencional en frijol común resulta difícil debido a que presenta una base genética estrecha y muy estable. En este sentido, la combinación de la mutagénesis y el cultivo de tejidos, es una alternativa para inducir variabilidad genética en la búsqueda de tolerancia a factores bióticos y abióticos. Es por ello, que el presente trabajo tuvo como objetivo determinar el efecto de diferentes explantes irradiados en la regeneración in vitro de frijol común (Phaseolus vulgaris L.) cultivar “ICA Pijao”. Se aplicaron radiaciones gamma en callos, en el nudo cotiledonal con un cotiledón (NC-1) con dosis de 0, 10, 20, 30, 40, 50 y 60 Gy y semillas con 0, 100, 200, 300 y 400 Gy. Se evaluó el porcentaje de germinación, longitud de las raíces, porcentaje de explantes que formaron callos, masa fresca (g) de los callos, número de brotes por callo y el número de brotes con raíces. La radiación gamma provocó una disminución en la masa fresca del callo y NC-1. Los callos y el NC-1 solamente formaron brotes con las dosis de 10 y 20 Gy, pero estos fueron hiperhíricos. Los resultados demostraron que la semilla irradiada fue el explante con el que se logró la regeneración in vitro de plantas con hojas definidas, por lo que se recomienda como explante inicial para el uso combinado de mutagénesis y regeneración in vitro de plantas para el cultivar P. vulgaris “ICA Pijao” a través de la organogénesis indirecta.

Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants

Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.

The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions

Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.

SnRK1 Kinase and the NAC Transcription Factor SOG1 Are Components of a Novel Signaling Pathway Mediating the Low Energy Response Triggered by ATP Depletion

Plant growth is strictly controlled by cell division, elongation, and differentiation for which adequate supplies of intracellular ATP are required. However, it is unclear how changes in the amount of intracellular ATP affect cell division and growth. To reveal the specific pathway dependent on ATP concentration, we performed analyses on the Arabidopsis mitochondria mutation sd3. The mutant is tiny, a result of a low amount of ATP caused by the disruption of Tim21, a subunit of the TIM23 protein complex localized in the inner membrane of the mitochondria. Loss of function of suppressor of gamma response 1 (SOG1) also restored the dwarf phenotype of wild type treated with antimycin A, a blocker of ATP synthesis in mitochondria. The sd3 phenotype is partially restored by the introduction of sog1, suppressor of gamma response 1, and kin10/kin11, subunits of Snf1-related kinase 1 (SnRK1). Additionally, SOG1 interacted with SnRK1, and was modified by phosphorylation in planta only after treatment with antimycin A. Transcripts of several negative regulators of the endocycle were up-regulated in the sd3 mutant, and this high expression was not observed in sd3sog1 and sd3kin11. We suggest that there is a novel regulatory mechanism for the control of plant cell cycle involving SnRK1 and SOG1, which is induced by low amounts of intracellular ATP, and controls plant development.

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.

Physiological and molecular studies on the effect of gamma radiation in fenugreek (Trigonella foenum-graecum L.) plants

This experiment assessed the biochemical changes in fenugreek plants exposed to gamma radiation. Two pot experiments were carried out during two growing seasons of 2015 and 2016. Seeds were subjected to five doses of gamma irradiation (25, 50, 100, 200 and 400 Gy) and were immediately planted into soil pots in a greenhouse. The experimental analysis was performed in M1 and M2 generations. Significant differences between irradiated and control plants were detected for most studied characters in M1 and M2 generations. It was demonstrated that low doses of gamma irradiation led to gradually increases in growth, yield characters, leaf soluble protein concomitantly with increases in the contents of phenolic and flavonoids compounds particularly at 100 Gy. These changes were accompanied by a substantial increase in ascorbic acid, α-tocopherol and retinol contents. Proline content was increased under all doses of gamma rays in M1 generation and the highest amount of proline was obtained at 200 Gy with visible decrease in M2 generation under the same dose. Meanwhile, the highest dose of gamma radiation (400 Gy) decreased all the studied parameters in both mutagenic generations as compared with control plants. In addition, gamma irradiation doses induced changes in DNA profile on using five primers and caused the appearance and disappearance of DNA polymorphic bands with variation in their intensity. These findings confirm the effectiveness of relatively low doses of gamma rays on improving the physiological and biochemical criteria of fenugreek plants.