Phenanthrene-responsive microRNAs and their targets in wheat roots

Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress

Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.

The roles of miR156 in abiotic and biotic stresses in plants

MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.

Exogenous IAA application affects the specific characteristics of fluoranthene distribution in Arabidopsis

Indole-3-acetic acid (IAA) is a crucial growth regulator involved in the accumulation of polycyclic aromatic hydrocarbons (PAHs). However, the precise physiological and molecular mechanisms underlying IAA-mediated plant growth and PAH accumulation are not yet fully understood. In this study, two distinct IAA-sensitive genotypes of Arabidopsis thaliana (wild type and Axr5 mutant) were chosen to investigate the mechanisms of fluoranthene (Flu) uptake and accumulation in plant tissues (roots and leaves) through physiological and molecular analyses. The results revealed that the Flu concentration in Axr5 leaves was significantly higher than that in wild-type (WT) leaves. In roots, the Flu content decreased significantly with increasing IAA treatment, while no significant changes were observed with lower IAA treatment. Principal component analysis demonstrated that Flu accumulation in Arabidopsis roots was associated with IAA concentrations, whereas Flu accumulation in leaves was dependent on the genotype. Moreover, Flu accumulation showed a positive correlation with the activity of glutathione S-transferase (GST) and root length and a positive correlation with catalase (CAT) and peroxidase (POD) activity in the leaves. Transcriptome analysis confirmed that the expression of the ethylene-related gene ATERF6 and GST-related genes ATGSTF14 and ATGSTU27 in roots, as well as the POD-related genes AtPRX9 and AtPRX25 and CAT-related gene AtCAT3 in leaves, played a role in Flu accumulation. Furthermore, WRKY transcription factors (TFs) in roots and NAC TFs in leaves were identified as important regulators of Flu accumulation. Understanding the mechanisms of Flu uptake and accumulation in A. thaliana provides valuable insights for regulating PAH accumulation in plants.

Expression Profiling of the Slow Rusting Resistance Genes Lr34/Yr18 and Lr67/Yr46 in Common Wheat (Triticum aestivum L.) and Associated miRNAs Patterns

The main efforts in common wheat (Triticum aestivum L.) breeding focus on yield, grain quality, and resistance to biotic and abiotic stresses. One of the major threats affecting global wheat cultivation and causing significant crop production losses are rust diseases, including leaf rust caused by a biotrophic fungus Puccinia triticina Eriks. Genetically determined resistance to leaf rust has been characterized in young plants (seedling resistance) as well as in plants at the adult plant stage. At the seedling stage, resistance is controlled vertically by major R genes, conferring a race-specific response that is highly effective but usually short-lived due to the rapid evolution of potentially virulent fungi. In mature plants, horizontal adult plant resistance (APR) was described, which provides long-term protection against multiple races of pathogens. A better understanding of molecular mechanisms underlying the function of APR genes would enable the development of new strategies for resistance breeding in wheat. Therefore, in the present study we focused on early transcriptomic responses of two major wheat APR genes, Lr34 and Lr67, and three complementary miRNAs, tae-miR9653b, tae-miR9773 and tae-miR9677b, to inoculation with P. triticina. Plant material consisted of five wheat reference varieties, Artigas, NP846, Glenlea, Lerma Rojo and TX89D6435, containing the Lr34/Yr18 and Lr67/Yr46 resistance genes. Biotic stress was induced by inoculation with fungal spores under controlled conditions in a phytotron. Plant material consisted of leaf tissue sampled before inoculation as well as 6, 12, 24 and 48 h postinoculation (hpi). The APR gene expression was quantified using real-time PCR with two reference genes, whereas miRNA was quantified using droplet digital PCR. This paper describes the resistance response of APR genes to inoculation with races of leaf rust-causing fungi that occur in central Europe. The study revealed high variability of expression profiles between varieties and time-points, with the prevalence of downregulation for APR genes and upregulation for miRNAs during the development of an early defense response. Nevertheless, despite the downregulation initially observed, the expression of Lr34 and Lr67 genes in studied cultivars was significantly higher than in a control line carrying wild (susceptible) alleles.

Recent allopolyploidy alters Spartina microRNA expression in response to xenobiotic-induced stress

Environmental contamination by xenobiotics represents a major threat for natural ecosystems and public health. In response, xenobiotic detoxification is a fundamental trait of organisms for developmental plasticity and stress tolerance, but the underlying molecular mechanisms remain poorly understood in plants. To decipher this process, we explored the consequences of allopolyploidy on xenobiotic tolerance in the genus Spartina Schreb. Specifically, we focused on microRNAs (miRNAs) owing to their central function in the regulation of gene expression patterns, including responses to stress. Small RNA-Seq was conducted on the parents S. alterniflora and S. maritima, their F1 hybrid S. x townsendii and the allopolyploid S. anglica under phenanthrene-induced stress (phe), a model Polycyclic Aromatic Hydrocarbon (PAH) compound. Differentially expressed miRNAs in response to phe were specifically identified within species. In complement, the respective impacts of hybridization and genome doubling were detected, through changes in miRNA expression patterns between S. x townsendii, S. anglica and the parents. The results support the impact of allopolyploidy in miRNA-guided regulation of plant response to phe. In total, we identified 17 phe-responsive miRNAs in Spartina among up-regulated MIR156 and down-regulated MIR159. We also describe novel phe-responsive miRNAs as putative Spartina-specific gene expression regulators in response to stress. Functional validation using Arabidopsis (L.) Heynh. T-DNA lines inserted in homologous MIR genes was performed, and the divergence of phe-responsive miRNA regulatory networks between Arabidopsis and Spartina was discussed.

Role of miR164 in the growth of wheat new adventitious roots exposed to phenanthrene

Polycyclic aromatic hydrocarbons (PAHs), ubiquitous organic pollutants in the environment, can accumulate in humans via the food chain and then harm human health. MiRNAs (microRNAs), a kind of non-coding small RNAs with a length of 18-30 nucleotides, regulate plant growth and development and respond to environmental stress. In this study, it is demonstrated that miR164 can regulate root growth and adventitious root generation of wheat under phenanthrene exposure by targeting NAC (NAM/ATAF/CUC) transcription factor. We observed that phenanthrene treatment accelerated the senescence and death of wheat roots, and stimulated the occurrence of new roots. However, it is difficult to compensate for the loss caused by old root senescence and death, due to the slower growth of new roots under phenanthrene exposure. Phenanthrene accumulation in wheat roots caused to generate a lot of reactive oxygen species, and enhanced lipoxygenase activity and malonaldehyde concentration, meaning that lipid peroxidation is the main reason for root damage. MiR164 was up-regulated by phenanthrene, enhancing the silence of NAC1, weakening the association with auxin signal, and inhibiting the occurrence of adventitious roots. Phenanthrene also affected the expression of CDK (the coding gene of cyclin-dependent kinase) and CDC2 (a gene regulating cell division cycle), the key genes in the cell cycle of pericycle cells, thereby affecting the occurrence and growth of lateral roots. In addition, NAM (a gene regulating no apical meristem) and NAC23 may also be related to the root growth and development in wheat exposed to phenanthrene. These results provide not only theoretical basis for understanding the molecular mechanism of crop response to PAHs accumulation, but also knowledge support for improving phytoremediation of soil or water contaminated by PAHs.

High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition

Soil salinization is one of the major abiotic stresses that adversely affect the yield and quality of crops such as wheat, a leading cereal crop worldwide. Excavating the salt-tolerant genes and exploring the salt tolerance mechanism can help breeding salt-tolerant wheat varieties. Thus, it is essential to identify salt-tolerant wheat germplasm resources. In this study, we carried out a salt stress experiment using Qing Mai 6 (QM6), a salt-tolerant wheat variety, and sequenced the miRNAs and mRNAs. The differentially expressed miRNAs and mRNAs in salt stress conditions were compared with the control. As results, a total of eight salt-tolerance-related miRNAs and their corresponding 11 target mRNAs were identified. Further analysis revealed that QM6 enhances salt tolerance through increasing the expression level of genes related to stress resistance, antioxidation, nutrient absorption, and lipid metabolism balance, and the expression of these genes was regulated by the identified miRNAs. The resulting data provides a theoretical basis for future research studies on miRNAs and novel genes related to salt tolerance in wheat in order to develop genetically improved salt-tolerant wheat varieties.

Transcriptomic and metabolomic insights into the adaptive response of Salix viminalis to phenanthrene

Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent environmental pollutants. They exert toxic effects at different developmental stages of plants. Plant defense mechanisms against PAHs are poorly understood. To this end, transcriptomics and widely targeted metabolomic sequencing were used to study the changes in gene expression and metabolites that occur in the roots of Salix viminalis subjected to phenanthrene stress. Significant variations in genes and metabolites were observed between treatment groups and the control group. Thirteen amino acids and key genes involved in their biosynthesis were upregulated exposed to phenanthrene. Cysteine biosynthesis was upregulated. Sucrose, inositol galactoside, and mellidiose were the main carbohydrates that were largely accumulated. Glutathione biosynthesis was enhanced in order to scavenge reactive oxygen species and detoxify the phenanthrene. Glucosinolate and flavonoid biosynthesis were upregulated. The production of pinocembrin, apigenin, and epigallocatechin increased, which may play a role in antioxidation to resist phenanthrene stress. In addition, levels of six amino acids and N,N'-(p-coumaroyl)-cinnamoyl-caffeoyl-spermidine were significantly increased, which may have helped protect the plant against phenanthrene stress. These results demonstrated that S. viminalis had a positive defense strategy in response to phenanthrene challenge. Subsequent defense-related reactions may have also occurred within 24 h of phenanthrene exposure. The findings of the present study would be useful in elucidating the molecular mechanisms regulating plant responses to PAH challenges and would help guide crop and plant breeders in enhancing PAH resistance.

Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.)

Potassium (K) is essential for plant growth and stress responses. MicroRNAs (miRNAs) are involved in adaptation to nutrient deprivation through modulating gene expression. Here, we identified the miRNAs responsive to K deficiency in Triticum aestivum based on high-throughput small RNA sequencing analyses. Eighty-nine miRNAs, including 68 previously reported ones and 21 novel ones, displayed differential expression under K deficiency. In Gene Ontology and Kyoto Encyclopedia and Genome analyses, the putative target genes of the differentially expressed miRNAs were categorized into functional groups associated with ADP-binding activity, secondary metabolic pathways, and biosynthesis and metabolism. Functional characterization of tae-miR408, an miRNA significantly down-regulated under K deficiency, revealed its important role in mediating low-K tolerance. Compared with wild type, transgenic tobacco lines overexpressing tae-miR408 showed significantly improved K uptake, biomass, photosynthesis, and reactive oxygen species scavenging under K deficiency. These results show that distinct miRNAs function in the plant response to K deficiency through regulating target genes involved in energy metabolism and various secondary metabolic pathways. Our findings shed light on the plant response to K deficiency mediated by miRNAs in T. aestivum. Distinct miRNAs, such as tae-miR408, are valuable targets for generating crop varieties with improved K-use efficiency.

Analysis of miRNA expression associated with the Lr46 gene responsible for APR resistance in wheat (Triticum aestivum L.)

Lr46/Yr29/Pm39 (Lr46) is a gene for slow rusting resistance in wheat. The aim of the study was to analyze the miRNA expression in selected common wheat cultivars carrying resistance genes, Lr46 among others (HN Rod, Pavon‘S’, Myna‘S’, Frontana‘S’, and Sparrow’S’) in response to leaf rust infection caused by Puccinia triticina Erikss. In the Pavon ‘S’, Myna ‘S’, Frontana‘S’, and Sparow‘S’ varieties a product with a length of 242 bp has been identified, which is specific to the Xwmc44 marker linked to the brown rust resistance gene Lr46. In the next step, the differences in the expression of microRNA (miR5085 and miR164) associated with the Lr46 gene, which is responsible for different resistance of selected wheat cultivars to leaf rust, were examined using emulsion PCR (ddPCR). In the experiment, biotic stress was induced in mature plants by infecting them with fungal spores under controlled conditions in a growth chamber. For analysis the plant material was collected before inoculation and 6, 12, 24, and 48 h after inoculation. The experiments also showed that plant infection with Puccinia triticina resulted in an increase in miR164 expression in cultivars carrying the Lr46 gene. The expression of miR164 remained stable in a control cultivar (HN ROD) lacking this gene. This has proved that miR164 can be involved in leaf rust resistance mechanisms.

miR398 is involved in the relief of phenanthrene-induced oxidative toxicity in wheat roots

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants and could produce oxidative toxicity to plants. Our previous study has shown that miR398 is involved in response to phenanthrene treatment by targeting CSD1 and CSD2. However, it is not clear which is essential for CSD1 and CSD2 and how miR398 changes. In this study, we performed discontinuous PAGE to separate superoxide dismutase (SOD) isozymes and found that two bands of the cytosolic Cu/Zn-SOD are induced by phenanthrene at day 5 and 7. Low expression of pri-miR398 and high expression of pre-miR398 indicate that the conversion process from pri-miR398 to pre-miR398 is impeded, which causes decrease in mature miR398. The relative expression of CSD1 is entirely up-regulated, further confirming the important role of CSD1 in response to phenanthrene exposure. Besides, the overexpression of WRKY implies its potential function in answering the call from phenanthrene stress. Therefore, it is concluded that the gene silencing of CSD1 recedes due to the biosynthesis inhibition of miR398, causing the increase of SOD activity in response to phenanthrene exposure in wheat roots. Our results are useful not only for better understanding miRNAs regulation in detoxication of reactive oxygen species, but also for alleviating the toxicity to crops caused by PAHs.

Combined toxic effects of microcystin-LR and phenanthrene on growth and antioxidant system of duckweed (Lemna gibba L.)

Microcystins and polycyclic aromatic hydrocarbons commonly co-exist in eutrophic freshwater environments. However, their combined toxicity remains unknown. The aim of this study was to evaluate the combined toxic effects of microcystin-LR (MC-LR) and phenanthrene (Phe) on duckweed (Lemna gibba L.) during a short-term exposure (7 d). L. gibba was exposed to a range of environmentally relevant concentrations of MC-LR (5, 50, 250, 500 μg/L) and Phe (0.1, 1, 5, 10 μg/L), both individually and in MC-LR + Phe mixtures (5 + 0.1, 50 + 1, 250 + 5, 500 + 10 μg/L). Subsequently, biomarkers of toxicity such as growth, chlorophyll-a, and antioxidant enzyme activity (catalase, superoxide dismutase, and peroxidase) were analyzed in L. gibba. Growth and the antioxidant system of L. gibba were not significantly inhibited by Phe alone, whereas higher concentrations of individual MC-LR (≥50 μg/L) significantly inhibited growth and induced oxidative stress. Based on Abott's formula, their interaction effects were concentration dependent. Antagonistic effects were observed when exposed to combinations of lower concentrations of MC-LR and Phe (≤50 + 1 μg/L), while additive or synergistic effects were induced at higher concentrations of both compounds (≥250 + 5 μg/L). Moreover, higher concentrations of Phe (≥5 μg/L) increased the accumulation of MC-LR in L. gibba. Our results suggested that the toxic effects of MC-LR and phenanthrene were exacerbated only when they co-exist in water bodies at relatively high concentrations. Consequently, co-existence of MC-LR and Phe at low levels are unlikely to exacerbate ecological hazards to L. gibba in most aquatic environments, at least based on responses of this plant.

Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat

Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal treatment while six were regulated in presence of it. The most represented miRNA family was miR167 that was regulated by water deficit in both leaf and root tissues. Interestingly, miR827-5p was differentially regulated in leaves in the absence of mycorrhizal treatment while it was water deficit-modulated in roots irrespective of AMF treatment. In roots, water deficit repressed miR827-5p, miR394, miR6187, miR167e-3p, and miR9666b-3p affecting transcription, RNA synthesis, protein synthesis, and protein modifications. In leaves, mycorrhizae modulated miR5384-3p and miR156e-3p affecting trafficking and cell redox homeostasis. DNA replication and transcription regulation should be targeted by the repression of miR1432-5p and miR166h-3p. This work provided interesting insights into the post-transcriptional mechanisms of wheat responses to water deficit in relation to mycorrhizal symbiosis.

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.