Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings

Exposure of Arabidopsis thaliana Mutants to Genotoxic Stress Provides New Insights for the Involvement of TDP1α and TDP1β genes in DNA-Damage Response

Genotoxic stress activates the DNA-damage response (DDR) signalling cascades responsible for maintaining genome integrity. Downstream DNA repair pathways include the tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme that hydrolyses the phosphodiester bond between the tyrosine of topoisomerase I (TopI) and 3'-phosphate of DNA. The plant TDP1 subfamily contains the canonical TDP1α gene and the TDP1β gene whose functions are not fully elucidated. The current study proposes to investigate the involvement of TDP1 genes in DDR-related processes by using Arabidopsis thaliana mutants treated with genotoxic agents. The phenotypic and molecular characterization of tdp1α, tdp1β and tdp1α/β mutants treated with cisplatin (CIS), curcumin (CUR), NSC120686 (NSC), zeocin (ZEO), and camptothecin (CPT), evidenced that while tdp1β was highly sensitive to CIS and CPT, tdp1α was more sensitive to NSC. Gene expression analyses showing upregulation of the TDP2 gene in the double mutant indicate the presence of compensatory mechanisms. The downregulation of POL2A gene in the tdp1β mutant along with the upregulation of the TDP1β gene in pol2a mutants, together with its sensitivity to replication inhibitors (CIS, CTP), point towards a function of this gene in the response to replication stress. Therefore, this study brings novel information relative to the activity of TDP1 genes in plants.

MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat

DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.

Exploring the putative microRNAs cross-kingdom transfer in Solanum lycopersicum-Meloidogyne incognita interactions

Introduction

Plant-pathogen interaction is an inexhaustible source of information on how to sustainably control diseases that negatively affect agricultural production. Meloidogyne incognita is a root-knot nematode (RKN), representing a pest for many crops, including tomato (Solanum lycopersicum). RKNs are a global threat to agriculture, especially under climate change, and RNA technologies offer a potential alternative to chemical nematicides. While endogenous microRNAs have been identified in both S. lycopersicum and M. incognita, and their roles have been related to the regulation of developmental changes, no study has investigated the miRNAs cross-kingdom transfer during this interaction.

Methods

Here, we propose a bioinformatics pipeline to highlight potential miRNA-dependent cross-kingdom interactions between tomato and M. incognita.

Results

The obtained data show that nematode miRNAs putatively targeting tomato genes are mostly related to detrimental effects on plant development and defense. Similarly, tomato miRNAs putatively targeting M. incognita biological processes have negative effects on digestion, mobility, and reproduction. To experimentally test this hypothesis, an in vitro feeding assay was carried out using sly-miRNAs selected from the bioinformatics approach. The results show that two tomato miRNAs (sly-miRNA156a, sly-miR169f) soaked by juvenile larvae (J2s) affected their ability to infect plant roots and form galls. This was also coupled with a significant downregulation of predicted target genes (Minc11367, Minc00111), as revealed by a qRT-PCR analysis.

Discussions

Therefore, the current study expands the knowledge related to the cross-kingdom miRNAs involvement in host-parasite interactions and could pave the way for the application of exogenous plant miRNAs as tools to control nematode infection.

Genotype-specific germination behavior induced by sustainable priming techniques in response to water deprivation stress in rice

Water stress brought about by climate change is among the major global concerns threatening food security. Rice is an important staple food which requires high water resources. Being a semi-aquatic plant, rice is particularly susceptible to drought. The aim of this work was to develop techniques directed to promote rice resilience to water deprivation stress during germination by implementing specific seed priming treatments. Five popular Italian rice varieties were subjected to priming treatments using novel, sustainable solutions, like poly-gamma-glutamic acid (γ-PGA), denatured γ-PGA (dPGA), and iron (Fe) pulsing, alone or in combination. The effect of the developed priming methods was tested under optimal conditions as well as under water deprivation stress imposed by polyethylene glycol (PEG) treatments. The priming efficacy was phenotypically determined in terms of germination behavior by measuring a series of parameters (germinability, germination index, mean germination time, seed vigor index, root and shoot length, germination stress tolerance index). Biochemical analyses were carried out to measure the levels of iron uptake and accumulation of reactive oxygen species (ROS). Integrative data analyses revealed that the rice varieties exhibited a strong genotype- and treatment-specific germination behavior. PEG strongly inhibited germination while most of the priming treatments were able to rescue it in all varieties tested except for Unico, which can be defined as highly stress sensitive. Molecular events (DNA repair, antioxidant response, iron homeostasis) associated with the transition from seed to seedling were monitored in terms of changes in gene expression profiles in two varieties sensitive to water deprivation stress with different responses to priming. The investigated genes appeared to be differentially expressed in a genotype-, priming treatment-, stress- and stage-dependent manner. The proposed seed priming treatments can be envisioned as sustainable and versatile agricultural practices that could help in addressing the impact of climate challenges on the agri-food system.

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.

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.

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.