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

Exogenous application of 5-azacitidin, royal jelly and folic acid regulate plant redox state, expression level of DNA methyltransferases and alleviate adverse effects of salinity stress on Vicia faba L. plants

DNA methylation is one of induced changes under salinity stress causing reduction in the expression of several crucial genes required for normal plant's operation. Potential use of royal jelly (RJ), folic acid (FA) and 5-azacitidine (5-AZA) on two Egyptian faba bean varieties (Sakha-3 and Giza-716) grown under saline conditions was investigated. Salinity stress affects negatively on seeds germination (G %), mitotic index, membrane stability and induced a significant increase in chromosomal abnormalities (CAs). DNA methyltransferases genes (MT1 and MT2) were highly up-regulated (∼23 and 8 folds for MT1 and MT2 in shoots of Giza-716 stressed plants). On the other hand, down regulation of other studied stress related genes: superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), heat shock protein (HSP-17.9) and proline-rich protein (GPRP) were detected in stressed plants of both studied varieties. Treating plants with RJ and FA increase G%, chlorophyll content, improves membrane properties and reduces CAs compared to non-treated stressed plants. Exogenous application of 5-AZA, RJ and FA on salinity stressed plants was associated with a significant reduction in the transcription of MT1 and MT2 which was associated with significant up regulation in the expression of Cu/Zn-SOD, CAT, GR, GPRP and HSP-17.9 encoding genes. The Lowest expression of MT1 and MT2 were induced with 5-AZA treatment in both studied varieties. Exogenous application of the FA, RJ and 5-AZA modified the methylation state of stressed plants by regulation the expression of DNA methyltransferases, subsequently, modulated the expression of studied genes and could be proposed as a promising treatment to ameliorate hazardous effects of salt stress on different plants.

SOG1 and BRCA1 Interdependently Regulate RAD54 Expression for Repairing Salinity-Induced DNA Double-Strand Breaks in Arabidopsis

As sessile organisms, land plants experience various forms of environmental stresses throughout their life span. Therefore, plants have developed extensive and complicated defense mechanisms, including a robust DNA damage response (DDR) and DNA repair systems for maintaining genome integrity. In Arabidopsis, the NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) plays an important role in regulating DDR. Here, we show that SOG1 plays a key role in regulating the repair of salinity-induced DNA double-strand breaks (DSBs) via the homologous recombination (HR) pathway in Arabidopsis. The sog1-1 mutant seedlings display a considerably slower rate of repair of salinity-induced DSBs. Accumulation of SOG1 protein increases in wild-type Arabidopsis under salinity stress, and it enhances the expression of HR pathway-related genes, including RAD51, RAD54 and BReast CAncer gene 1 (BRCA1), respectively, as found in SOG1 overexpression lines. SOG1 binds specifically to the AtRAD54 promoter at the 5'-(N)4GTCAA(N)3C-3' consensus sequence and positively regulates its expression under salinity stress. The phenotypic responses of sog1-1/atrad54 double mutants suggest that SOG1 functions upstream of RAD54, and both these genes are essential in regulating DDR under salinity stress. Furthermore, SOG1 interacts directly with BRCA1, an important component of the HR-mediated DSB repair pathway in plants, where BRCA1 appears to facilitate the binding of SOG1 to the RAD54 promoter. At the genetic level, SOG1 and BRCA1 function interdependently in modulating RAD54 expression under salinity-induced DNA damage. Together, our results suggest that SOG1 regulates the repair of salinity-induced DSBs via the HR-mediated pathway through genetic interactions with RAD54 and BRCA1 in Arabidopsis.

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.

Ameliorating effect of nanoparticles and seeds' heat pre-treatment on soybean plants exposed to sea water salinity

Impairing plant growth and reducing crop production, salinity is considered as major problem in modern agriculture. The current study aimed to investigate the role of seeds' heat pretreatment at 45 °C as well as application of two different nanoparticles nanosilica (N1) and nanoselenium (N2) in reducing salinity stress in three genotypes of Egyptian commercial soybeans (Glycine max L.). Two levels of salt stress using diluted sea water (1/12 and 1/6) were tested either alone or in combination with protective treatments. Obtained results revealed that salinity caused a significant reduction in all tested physiological parameters such as germination rate and membrane stability in soybean plants. A significant reduction in mitotic index and arrest in metaphase were recorded under both tested levels of salinity. It was also revealed that chromosomal abnormalities in soybean plants were positively correlated with the applied salinity concentrations. The fragmentation effect of salinity on the nuclear DNA was investigated and confirmed using Comet assay analysis. Seeds heat pre-treatment (45 °C) and both types of nanoparticles' treatments yielded positive effects on both the salt-stressed and unstressed plants. Quantitative real-time reverse transcription PCR (qRT-PCR) analysis for salt stress responsive marker genes revealed that most studied genes (CAT, APX, DHN2, CAB3, GMPIPL6 and GMSALT3) responded favorably to protective treatments. The modulation in gene expression pattern was associated with improving growth vigor and salinity tolerance in soybean plants. Our results suggest that seeds' heat pretreatment and nanoparticle applications support the recovery against oxidative stresses and represent a promising strategy for alleviating salt stress in soybean genotypes.

Endoreduplication in plant organogenesis: a means to boost fruit growth

Endoreduplication is the major source of somatic endopolyploidy in higher plants, and leads to variation in cell ploidy levels due to iterative rounds of DNA synthesis in the absence of mitosis. Despite its ubiquitous occurrence in many plant organs, tissues, and cells, the physiological meaning of endoreduplication is not fully understood, although several roles during plant development have been proposed, mostly related to cell growth, differentiation, and specialization via transcriptional and metabolic reprogramming. Here, we review recent advances in our knowledge of the molecular mechanisms and cellular characteristics of endoreduplicated cells, and provide an overview of the multi-scale effects of endoreduplication on supporting growth in plant development. In addition, the effects of endoreduplication in fruit development are discussed, since it is highly prominent during fruit organogenesis where it acts as a morphogenetic factor supporting rapid fruit growth, as illustrated by case of the model fleshy fruit, tomato (Solanum lycopersicum).

Endoreplication-Why Are We Not Using Its Full Application Potential?

Endoreplication-a process that is common in plants and also accompanies changes in the development of animal organisms-has been seen from a new perspective in recent years. In the paper, we not only shed light on this view, but we would also like to promote an understanding of the application potential of this phenomenon in plant cultivation. Endoreplication is a pathway for cell development, slightly different from the classical somatic cell cycle, which ends with mitosis. Since many rounds of DNA synthesis take place within its course, endoreplication is a kind of evolutionary compensation for the relatively small amount of genetic material that plants possess. It allows for its multiplication and active use through transcription and translation. The presence of endoreplication in plants has many positive consequences. In this case, repeatedly produced copies of genes, through the corresponding transcripts, help the plant acquire the favorable properties for which proteins are responsible directly or indirectly. These include features that are desirable in terms of cultivation and marketing: a greater saturation of fruit and flower colors, a stronger aroma, a sweeter fruit taste, an accumulation of nutrients, an increased resistance to biotic and abiotic stress, superior tolerance to adverse environmental conditions, and faster organ growth (and consequently the faster growth of the whole plant and its biomass). The two last features are related to the nuclear-cytoplasmic ratio-the greater the content of DNA in the nucleus, the higher the volume of cytoplasm, and thus the larger the cell size. Endoreplication not only allows cells to reach larger sizes but also to save the materials used to build organelles, which are then passed on to daughter cells after division, thus ending the classic cell cycle. However, the content of genetic material in the cell nucleus determines the number of corresponding organelles. The article also draws attention to the potential practical applications of the phenomenon and the factors currently limiting its use.

A novel transcription factor, BmZFP67, regulates endomitosis switch by controlling the expression of cyclin B in silk glands

Endomitosis is involved in developmental processes associated with an increase in metabolic cell activity, which is characterized by repeated rounds of DNA replication without cytokinesis. Endomitosis cells are widespread in protozoa, plants, animals and humans. Endomitosis cell cycle is currently viewed as a variation of the canonical cell cycle and transformed from mitotic cell cycle. However, the meaningful question about how endomitosis transformed from mitosis is still unclear. Herein, we identified a novel transcription factor in silk glands, ZFP67, which is gradually reduced in silk glands during the transition of mitosis to endomitosis. In addition, over-expressed ZFP67 in silk glands led to the transition delayed. And, knock-out of ZFP67 led to abnormal chromatin division and unsuccessful cell division. These data reveled that ZFP67 played an important role in transition of mitosis to endomitosis. Furthermore, ZFP67 can regulate the transcription of cyclin B, a key cyclin related to cell division and G2/M phase, which is demonstrated by chromatin immunoprecipitation and dual luciferase reporter system in this article. In conclusion, it can be speculated that the decreasing expression of ZFP67 in silk glands during the transition stage of mitosis-to-endomitosis resulted in the lack of cyclin B, which further led to unsuccessful cytokinesis and then promoted the transition from mitosis to endomitosis of silk gland cells.

ATM and ATR, two central players of the DNA damage response, are involved in the induction of systemic acquired resistance by extracellular DNA, but not the plant wound response

Background

The plant immune response to DNA is highly self/nonself-specific. Self-DNA triggered stronger responses by early immune signals such as H2O2 formation than nonself-DNA from closely related plant species. Plants lack known DNA receptors. Therefore, we aimed to investigate whether a differential sensing of self-versus nonself DNA fragments as damage- versus pathogen-associated molecular patterns (DAMPs/PAMPs) or an activation of the DNA-damage response (DDR) represents the more promising framework to understand this phenomenon.

Results

We treated Arabidopsis thaliana Col-0 plants with sonicated self-DNA from other individuals of the same ecotype, nonself-DNA from another A. thaliana ecotype, or nonself-DNA from broccoli. We observed a highly self/nonself-DNA-specific induction of H2O2 formation and of jasmonic acid (JA, the hormone controlling the wound response to chewing herbivores) and salicylic acid (SA, the hormone controlling systemic acquired resistance, SAR, to biotrophic pathogens). Mutant lines lacking Ataxia Telangiectasia Mutated (ATM) or ATM AND RAD3-RELATED (ATR) - the two DDR master kinases - retained the differential induction of JA in response to DNA treatments but completely failed to induce H2O2 or SA. Moreover, we observed H2O2 formation in response to in situ-damaged self-DNA from plants that had been treated with bleomycin or SA or infected with virulent bacteria Pseudomonas syringae pv. tomato DC3000 or pv. glycinea carrying effector avrRpt2, but not to DNA from H2O2-treated plants or challenged with non-virulent P. syringae pv. glycinea lacking avrRpt2.

Conclusion

We conclude that both ATM and ATR are required for the complete activation of the plant immune response to extracellular DNA whereas an as-yet unknown mechanism allows for the self/nonself-differential activation of the JA-dependent wound response.

The plant-specific DDR factor SOG1 increases chromatin mobility in response to DNA damage

Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observe an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. This increase in mobility is lost in the sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Also, DSB sites show particularly high mobility levels and their enhanced mobility requires the HR factor RAD54. Our data suggest that repair mechanisms promote chromatin mobility upon DNA damage, implying a role of this process in the early steps of the DNA damage response.

Transcriptomic analysis reveals the role of FOUR LIPS in response to salt stress in rice

An R2R3-MYB transcription factor FOUR LIPS associated with B-type Cyclin-Dependent Kinase 1;1 confers salt tolerance in rice. The Arabidopsis FOUR LIPS (AtFLP), an R2R3 MYB transcription factor, acts as an important stomatal development regulator. Only one orthologue protein of AtFLP, Oryza sativa FLP (OsFLP), was identified in rice. However, the function of OsFLP is largely unknown. In this study, we conducted RNA-seq and ChIP-seq to investigate the potential role of OsFLP in rice. Our results reveal that OsFLP is probably a multiple functional regulator involved in many biological processes in growth development and stress responses in rice. However, we mainly focus on the role of OsFLP in salt stress response. Consistently, phenotypic analysis under salt stress conditions showed that osflp exhibited significant sensitivity to salt stress, while OsFLP over-expression lines displayed obvious salt tolerance. Additionally, Yeast one-hybrid assay and electrophoretic mobility shift assay (EMSA) showed that OsFLP directly bound to the promoter region of Oryza sativa B-type Cyclin-Dependent Kinase 1;1 (OsCDKB1;1), and the expression of OsCDKB1;1 was repressed in osflp. Disturbing the expression of OsCDKB1;1 remarkably enhanced the tolerance to salt stress. Taken together, our findings reveal a crucial function of OsFLP regulating OsCDKB1;1 in salt tolerance and largely extend the knowledge about the role of OsFLP in rice.

Nitric oxide mediated regulation of ascorbate-glutathione pathway alleviates mitotic aberrations and DNA damage in Allium cepa L. under salinity stress

Allium cepa L. is an important medicinal and food plant enormously affected by salinity in terms of its growth and quality. This experiment investigates ameliorative potential of NO donor sodium nitroprusside (SNP) on chromosomal aberrations and physiological parameters in A. cepa L. roots exposed to salinity stress. Roots with different concentrations of NaCl (25, 50, and 100 mM) alone, and in combination with 100 µM SNP were analyzed for mitotic aberrations, DNA damage, proline, malondialdehyde (MDA) content, and ascorbate-glutathione (AsA-GSH) cycle after 120 h of salinity treatments. Results revealed that salinity stress increased chromosomal aberrations, MDA, proline accumulation, and severely hampered the AsA-GSH cycle function. The comet assay revealed a significant (p ≤ 0.05) enhancement in tail length (4.35 ± 0.05 µm) and olive tail moment (3.19 ± 0.04 µm) at 100 mM NaCl exposure. However, SNP supplementation decreased total percent abnormalities, while increased the prophase, metaphase, anaphase, and telophase indexes. Moreover, ascorbate peroxidase and glutathione reductase activities increased with AsA/DHA and GSH/GSSG ratios, respectively. Results suggest that SNP supplementation alleviates salinity stress responses by improving AsA-GSH cycle and proline accumulation. Based on present findings, NO supplementation could be recommended as a promising approach for sustainable crop production under salinity stress.

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.

Plant CDKs-Driving the Cell Cycle through Climate Change

In a growing population, producing enough food has become a challenge in the face of the dramatic increase in climate change. Plants, during their evolution as sessile organisms, developed countless mechanisms to better adapt to the environment and its fluctuations. One important way is through the plasticity of their body and their forms, which are modulated during plant growth by accurate control of cell divisions. A family of serine/threonine kinases called cyclin-dependent kinases (CDK) is a key regulator of cell divisions by controlling cell cycle progression. In this review, we compile information on the primary response of plants in the regulation of the cell cycle in response to environmental stresses and show how the cell cycle proteins (mainly the cyclin-dependent kinases) involved in this regulation can act as components of environmental response signaling cascades, triggering adaptive responses to drive the cycle through climate fluctuations. Understanding the roles of CDKs and their regulators in the face of adversity may be crucial to meeting the challenge of increasing agricultural productivity in a new climate.