Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

MicroRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice

MicroRNAs (miRNAs) are small noncoding RNAs that play a vital role in plant responses to abiotic and biotic stresses. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stresses, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its target SPL genes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression of miPEP156e led to decreased uptake and accumulation of Cd and reactive oxygen species (ROS) levels in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines. Conversely, miPEP156e mutants displayed sensitivity to Cd stress due to the elevated accumulation of Cd and ROS. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter genes and ROS scavenging genes. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.

Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review

Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.

Screening and validation of optimal miRNA reference genes in different developing stages and tissues of Lilium henryi Baker

Dynamic miRNA detection using the qRT-PCR technique requires appropriate reference genes to ensure data reliability. Previous studies have screened internal reference genes in plants during embryonic development and various stress treatment, involving relatively few tissues and organs. There is no relevant miRNA study in Lilium henryi Baker and limited research on the optimal miRNA reference genes in lilies, such as 5S, 18S, U6 and Actin. Twelve genes were selected as candidate reference genes whose expression stability was analyzed in petals at different developmental stages and other tissues using various algorithms, such as geNorm, NormFinder, BestKeeper, and Delta CT. The results revealed that the optimal combination of reference genes for Lilium henryi Baker petals at different developmental stages was osa-miR166m and osa-miR166a-3p, while that for different tissues of Lilium henryi Baker was osa-miR166g-3p and osa-miR166a-3p.Four important genes related to growth and development regulation, namely, osa-miR156a, osa-miR395b, osa-miR396a-3p, and osa-miR396a-5p, were selected for validation. The findings of the present study could contribute to future investigations onmiRNA expression and the related functions in Lilium henryi Baker while providing important references for the normalization of the miRNA expression in other varieties of lily.

Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum

Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.

Spatial transcriptomics drives a new era in plant research

The plant community lags far behind the animal and human fields concerning the application of single‐cell methodologies. This is primarily due to the challenges associated with plant tissue dissection and the limitations of the available technologies. However, recent advances in spatial transcriptomics enable the study of single‐cells derived from plant tissues from a spatial perspective. This technology is already successfully used to identify cell types, reconstruct cell‐fate lineages, and reveal cell‐to‐cell interactions. Future technological advancements will overcome the challenges in sample processing, data analysis, and the integration of multiple‐omics technologies. Thanks to spatial transcriptomics, we anticipate several plant research projects to significantly advance our understanding of critical aspects of plant biology.

Role of mi RNA in Phytoremediation of Heavy Metals and Metal Induced Stress Alleviation

Anthropogenic activities have contributed hugely in enhancing various types of environmental toxicity. One of these is higher accumulation of toxic heavy metals in soil and plant tissues. Although many heavy metals act as essential component for the growth and development of plants when present in low concentrations but at higher concentrations it becomes cytotoxic. Several innate mechanisms have evolved in plants to cope with it. In recent years the mechanism of using miRNA to combat metal induced toxicity has come to fore front. The miRNA or the microRNA regulates different physiological processes and induces a negative control in expressing the complementary target genes. The cleavage formation by post-transcriptional method and the inhibition of targeted translational mRNA are the two main procedures by which plant miRNAs function. The heavy and enhanced metal accumulation in plants has increased the production of different kinds of free radicals like reactive nitrogen and oxygen which damage the plants oxidatively. Several plant miRNA are capable of targeting and reducing the expression of those genes which are responsible for higher metal accumulation and storage. This can reduce the metal load and hence its negative impact on plant can also be reduced. This review depicts the biogenesis, the mode of action of miRNA, and the control mechanisms of miRNA in metal induced stress response in plant. A detailed review on the role of plant miRNA in alleviation of metal induced stress is discussed in this present study.

Response to Cadmium Toxicity: Orchestration of Polyamines and microRNAs in Maize Plant

Cadmium (Cd) is a heavy metal that is widely contaminating the environment due to its uses in industries as corrosive reagents, paints, batteries, etc. Cd can easily be absorbed through plant roots and may have serious negative impacts on plant growth. To investigate the mechanisms utilized by plants to cope with Cd toxicity, an experiment was conducted on maize seedlings. We observed that the plant growth and photosynthetic mechanism were negatively influenced during 20 days of Cd stress. The expression levels of ornithine decarboxylase (ORDC) increased in the six seedlings under Cd exposure compared to the control. However, Cd toxicity led to an increase in putrescine (Put) content only on day 15 when compared to the control plants. In fact, with the exception of day 15, the increases in the ORDC transcript levels did not show a direct correlation with the observed increases in Put content. Spermidine and Spermine levels were reduced on day 6 by Cd application, which was parallel with suppressed Spermidine synthase gene. However, an increase in Spermidine and Spermine levels was observed on day 12 along with a significant elevation in Spermidine synthase expression. On day 6, Cd was observed to start accumulating in the root with an increase in the expression of microRNA 528; while on day 15, Cd started to be observed in the shoot part with an increase in microRNA 390 and microRNA 168. These results imply that different miRNAs may regulate polyamines (PAs) in maize under Cd toxicity, suggesting a plant-derived strategy to commit a PAs/miRNA-regulated mechanism/s in different developmental stages (time points) in response to Cd exposure.

Detoxifying the heavy metals: a multipronged study of tolerance strategies against heavy metals toxicity in plants

Heavy metal concentrations exceeding permissible limits threaten human life, plant life, and all other life forms. Different natural and anthropogenic activities emit toxic heavy metals in the soil, air, and water. Plants consume toxic heavy metals from their roots and foliar part inside the plant. Heavy metals may interfere with various aspects of the plants, such as biochemistry, bio-molecules, and physiological processes, which usually translate into morphological and anatomical changes. They use various strategies to deal with the toxic effects of heavy metal contamination. Some of these strategies include restricting heavy metals to the cell wall, vascular sequestration, and synthesis of various biochemical compounds, such as phyto-chelators and organic acids, to bind the free moving heavy metal ions so that the toxic effects are minimized. This review focuses on several aspects of genetics, molecular, and cell signaling levels, which integrate to produce a coordinated response to heavy metal toxicity and interpret the exact strategies behind the tolerance of heavy metals stress. It is suggested that various aspects of some model plant species must be thoroughly studied to comprehend the approaches of heavy metal tolerance to put that knowledge into practical use.

Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses

Metal tolerance proteins (MTPs) as Me²⁺/H⁺(K⁺) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd²⁺ and Cu²⁺ exposure might be responsible for metal translocation from roots to leaves.

MicroRNA miR171b Positively Regulates Resistance to Huanglongbing of Citrus

Huanglongbing (HLB) is one of the most severe citrus diseases in the world, causing huge economic losses. However, efficient methods of protecting citrus from HLB have not yet been developed. microRNA (miRNA)-mediated regulation of gene expression is a useful tool to control plant diseases, but the miRNAs involved in regulating resistance to HLB have not yet been identified. In this study, we found that miR171b positively regulated resistance to HLB in citrus. Upon infection with HLB bacteria, the bacteria were detected in the second month in the control plants. However, in the miR171b-overexpressing transgenic citrus plants, the bacteria could not be detected until the 24th month. RNA-seq data indicated that multiple pathways, such as photosynthesis, plant–pathogen interaction, the MAPK signaling pathway, etc., might be involved in improving the resistance to HLB in miR171b-overexpressing plants compared with the control. Finally, we determined that miR171b could target SCARECROW-like (SCL) genes to downregulate their expression, which then led to promoted resistance to HLB stress. Collectively, our results demonstrate that miR171b plays a positive regulatory role in resistance to citrus HLB, and provides a new insight into the role of miRNAs in the adaptation of citrus to HLB stress.

Identification and characterization of CircRNA-associated CeRNA networks in moso bamboo under nitrogen stress

BACKGROUND

Nitrogen is a macronutrient element for plant growth and development. Circular RNAs (circRNAs) serve as pivotal regulators for the coordination between nutrient supply and plant demand. Moso bamboo (Phyllostachys edulis) is an excellent plant with fast growth, and the mechanism of the circRNA-target module in response to nitrogen remains unclear.

RESULTS

Deep small RNA sequencing results of moso bamboo seedlings under different concentrations of KNO₃ (N0 = 0 mM, N6 = 6 mM, N18 = 18 mM) were used to identify circRNAs. A total of 549 circRNAs were obtained, of which 309 were generated from corresponding parental coding genes including 66 new ones. A total of 536 circRNA-parent genes were unevenly distributed in 24 scaffolds and were associated with root growth and development. Furthermore, 52 differentially expressed circRNAs (DECs) were obtained, including 24, 33 and 15 DECs from three comparisons of N0 vs. N6, N0 vs. N18 and N6 vs. N18, respectively. Based on integrative analyses of the identified DECs, differentially expressed mRNAs (DEGs), and miRNAs (DEMs), a competitive endogenous RNA (ceRNA) network was constructed, including five DECs, eight DEMs and 32 DEGs. A regulatory module of PeSca_6:12,316,320|12,372,905-novel_miR156-PH02Gene35622 was further verified by qPCR and dual-luciferase reporter assays.

CONCLUSION

The results indicated that circRNAs could participate in multiple biological processes as miRNA sponges, including organ nitrogen compound biosynthesis and metabolic process regulation in moso bamboo. Our results provide valuable information for further study of circRNAs in moso bamboo under fluctuating nitrogen conditions.

Specific alterations in riboproteomes composition of isonicotinic acid treated arabidopsis seedlings

Plants have developed strategies to deal with the great variety of challenges they are exposed to. Among them, common targets are the regulation of transcription and translation to finely modulate protein levels during both biotic and abiotic stresses. Increasing evidence suggests that ribosomes are highly adaptable modular supramolecular structures which remodel to adapt to stresses. Each Arabidopsis thaliana ribosome consists of approximately 81 distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. To investigate the identity of ribosomal proteins of the small subunit (RPS) and of the large subunit (RPL) as well as ribosomes-associated proteins, we analysed by LC/MS/MS immunopurified ribosomes from A. thaliana leaves treated with isonicotinic acid (INA), an inducer of plant innate immunity. We quantified a total of 2084 proteins. 165 ribosome-associated proteins showed increased abundance while 52 were less abundant. Of the 52 identified RPS (from a possibility of 104 encoding genes), 15 were deregulated. Similarly, from the 148 possible RPL, 80 were detected and 9 were deregulated. Our results revealed potential candidates involved in innate immunity that could be interesting targets for functional genomic studies.

Transcriptional Regulatory Network of Plant Cadmium Stress Response

Cadmium (Cd) is a non-essential heavy metal with high toxicity to plants. Plants have acquired specialized mechanisms to sense, transport, and detoxify Cd. Recent studies have identified many transporters involved in Cd uptake, transport, and detoxification. However, the complex transcriptional regulatory networks involved in Cd response remain to be elucidated. Here, we provide an overview of current knowledge regarding transcriptional regulatory networks and post-translational regulation of the transcription factors involved in Cd response. An increasing number of reports indicate that epigenetic regulation and long non-coding and small RNAs are important in Cd-induced transcriptional responses. Several kinases play important roles in Cd signaling that activate transcriptional cascades. We also discuss the perspectives to reduce grain Cd content and improve crop tolerance to Cd stress, which provides a theoretical reference for food safety and the future research of plant varieties with low Cd accumulation.

Metal-responsive elements confer cadmium response in Arabidopsis

Molecular, biochemical, and genetic experiments demonstrate that metal-responsive elements (MREs), initially identified in animals, confer the cadmium transcriptional response in Arabidopsis, thus providing deep functional insights of MREs in plants. Cadmium (Cd) is highly toxic to all organisms including plants. Cd-responsive gene transcription is a fundamental aspect of the Cd response, in which Cd stress regulatory cis-acting elements are essential. However, little is known regarding such elements in plants. Metal-responsive elements (MREs, 5'-TGCRCNC-3', R: A or G, N: any base) are essential for transcriptional induction of Cd in animals. MREs are also contained in the promoters of some Cd-regulated plant genes, but whether MREs confer Cd responses in plants is poorly defined. Herein, we used a previously identified MRE of the tobacco feedback-insensitive anthranilate synthase α-2 chain gene as a representative MRE (named as MREa, 5'-TGCACAC-3') to explore the roles of MREs in the transcriptional response to Cd stress in Arabidopsis thaliana. First, we showed that MREa conferred Cd stress responsiveness on a minimal promoter in both concentration- and time-dependent manners, whereas the mutated MREa did not. Second, MREa specifically bound nuclear extracts, displaying a biochemical characteristic of cis-acting elements. We screened and identified four MREa-binding transcription factors, including ethylene response factor 13 (AtERF13). At last, MREa could mediate AtERF13 to activate the β-glucuronidase (GUS) reporter expression. Overall, these molecular, biochemical, and genetic data suggest that MREa is instrumental in the Cd response in Arabidopsis, thus providing deep functional insights of MREs in plants.

Molecular mechanisms underlying the toxicity and detoxification of trace metals and metalloids in plants

Plants take up a wide range of trace metals/metalloids (hereinafter referred to as trace metals) from the soil, some of which are essential but become toxic at high concentrations (e.g., Cu, Zn, Ni, Co), while others are non-essential and toxic even at relatively low concentrations (e.g., As, Cd, Cr, Pb, and Hg). Soil contamination of trace metals is an increasing problem worldwide due to intensifying human activities. Trace metal contamination can cause toxicity and growth inhibition in plants, as well as accumulation in the edible parts to levels that threatens food safety and human health. Understanding the mechanisms of trace metal toxicity and how plants respond to trace metal stress is important for improving plant growth and food safety in contaminated soils. The accumulation of excess trace metals in plants can cause oxidative stress, genotoxicity, programmed cell death, and disturbance in multiple physiological processes. Plants have evolved various strategies to detoxify trace metals through cell-wall binding, complexation, vacuolar sequestration, efflux, and translocation. Multiple signal transduction pathways and regulatory responses are involved in plants challenged with trace metal stresses. In this review, we discuss the recent progress in understanding the molecular mechanisms involved in trace metal toxicity, detoxification, and regulation, as well as strategies to enhance plant resistance to trace metal stresses and reduce toxic metal accumulation in food crops.

Genetic Regulation Mechanism of Cadmium Accumulation and Its Utilization in Rice Breeding

Cadmium (Cd) is a heavy metal whose pollution in rice fields leads to varying degrees of Cd accumulation in rice. Furthermore, the long-term consumption of Cd-contaminated rice is harmful to human health. Therefore, it is of great theoretical significance and application value to clarify the genetic regulation mechanism of Cd accumulation in rice and cultivate rice varieties with low Cd accumulation for the safe use of Cd-contaminated soils. This review summarizes the effects of Cd on rice growth, yield, and quality; the physiological and molecular mechanisms of Cd absorption in the roots, loading, and transport of Cd in the xylem, the distribution of Cd in nodes, redistribution of Cd in leaves, and accumulation of Cd in the grains; the regulation mechanism of the Cd stress response; and the breeding of rice with low Cd accumulation. Future directions on the genetic regulation of Cd in rice and application are also discussed. This review provides a theoretical basis for studies exploring the genetic regulation of Cd stress in rice. It also offers a basis for formulating effective strategies to reduce the Cd content in rice.

Integrated High-Throughput Sequencing, Microarray Hybridization and Degradome Analysis Uncovers MicroRNA-Mediated Resistance Responses of Maize to Pathogen Curvularia lunata

Curvularia lunata (Wakker) Boed, the causal agent of leaf spot in maize, is prone to mutation, making it difficult to control. RNAi technology has proven to be an important tool of genetic engineering and functional genomics aimed for crop improvement. MicroRNAs (miRNAs), which act as post-transcriptional regulators, often cause translational repression and gene silencing. In this article, four small RNA (sRNA) libraries were generated from two maize genotypes inoculated by C. lunata; among these, ltR1 and ltR2 were from the susceptible variety Huangzao 4 (HZ), ltR3 and ltR4, from the resistant variety Luyuan (LY), and 2286, 2145, 1556 and 2504 reads were annotated as miRNA in these four sRNA libraries, respectively. Through the combined analysis of high-throughput sequencing, microarray hybridization and degradome, 48 miRNAs were identified as being related to maize resistance to C. lunata. Among these, PC-732 and PC-169, two new maize miRNAs discovered, were predicted to cleave mRNAs of metacaspase 1 (AMC1) and thioredoxin family protein (Trx), respectively, possibly playing crucial roles in the resistance of maize to C. lunata. To further confirm the role of PC-732 in the interaction of maize and C. lunata, the miRNA was silenced through STTM (short tandem target mimic) technology, and we found that knocking down PC-732 decreased the susceptibility of maize to C. lunata. Precisely speaking, the target gene of PC-732 might inhibit the expression of disease resistance-related genes during the interaction between maize and C. lunata. Overall, the findings of this study indicated the existence of miRNAs involved in the resistance of maize to C. lunata and will contribute to rapidly clarify the resistant mechanism of maize to C. lunata.

Plant responses to metals stress: microRNAs in focus

Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.

Integrative analyses of morphology, physiology, and transcriptional expression profiling reveal miRNAs involved in culm color in bamboo

Culm color variation is an interesting phenomenon that contributes to the breeding of new varieties of ornamental plants during domestication. De-domesticated variation is considered ideal for identifying and interpreting the molecular mechanisms of plant mutations. However, the variation in culm color of bamboo remains unknown. In the present study, yellow and green culms generated from the same rhizome of Phyllostachys vivax cv. Aureocaulis (P. vivax) were used to elucidate the molecular mechanism of culm color formation. Phenotypic and physiological data showed that environmental suitability was higher in green culms than in yellow culms. High-throughput sequencing analysis showed 295 differentially expressed genes (DEGs) and 22 differentially expressed miRNAs (DEMs) in two different colored bamboo culms. There were 103 DEM-DEG interaction pairs, of which a representative "miRNA-mRNA" regulatory module involved in photosynthesis and pigment metabolism was formed by 14 DEM-DEG pairs. The interaction of the three key pairs was validated by qPCR and dual-luciferase assays. This study provides new insights into the molecular mechanism of miRNAs involved in P. vivax culm color formation, which provides evidence for plant de-domestication and is helpful for revealing the evolutionary mechanism of bamboo.

Natural Molecular Mechanisms of Plant Hyperaccumulation and Hypertolerance towards Heavy Metals

The main mechanism of plant tolerance is the avoidance of metal uptake, whereas the main mechanism of hyperaccumulation is the uptake and neutralization of metals through specific plant processes. These include the formation of symbioses with rhizosphere microorganisms, the secretion of substances into the soil and metal immobilization, cell wall modification, changes in the expression of genes encoding heavy metal transporters, heavy metal ion chelation, and sequestration, and regenerative heat-shock protein production. The aim of this work was to review the natural plant mechanisms that contribute towards increased heavy metal accumulation and tolerance, as well as a review of the hyperaccumulator phytoremediation capacity. Phytoremediation is a strategy for purifying heavy-metal-contaminated soils using higher plants species as hyperaccumulators.

The Homeodomain-Leucine Zipper Genes Family Regulates the Jinggangmycin Mediated Immune Response of Oryza sativa to Nilaparvata lugens, and Laodelphax striatellus

The homeodomain-leucine zipper (HDZIP) is an important transcription factor family, instrumental not only in growth but in finetuning plant responses to environmental adversaries. Despite the plethora of literature available, the role of HDZIP genes under chewing and sucking insects remains elusive. Herein, we identified 40 OsHDZIP genes from the rice genome database. The evolutionary relationship, gene structure, conserved motifs, and chemical properties highlight the key aspects of OsHDZIP genes in rice. The OsHDZIP family is divided into a further four subfamilies (i.e., HDZIP I, HDZIP II, HDZIP III, and HDZIP IV). Moreover, the protein–protein interaction and Gene Ontology (GO) analysis showed that OsHDZIP genes regulate plant growth and response to various environmental stimuli. Various microRNA (miRNA) families targeted HDZIP III subfamily genes. The microarray data analysis showed that OsHDZIP was expressed in almost all tested tissues. Additionally, the differential expression patterns of the OsHDZIP genes were found under salinity stress and hormonal treatments, whereas under brown planthopper (BPH), striped stem borer (SSB), and rice leaf folder (RLF), only OsHDZIP3, OsHDZIP4, OsHDZIP40, OsHDZIP10, and OsHDZIP20 displayed expression. The qRT-PCR analysis further validated the expression of OsHDZIP20, OsHDZIP40, and OsHDZIP10 under BPH, small brown planthopper (SBPH) infestations, and jinggangmycin (JGM) spraying applications. Our results provide detailed knowledge of the OsHDZIP gene family resistance in rice plants and will facilitate the development of stress-resilient cultivars, particularly against chewing and sucking insect pests.

microRNAs: Key Players in Plant Response to Metal Toxicity

Environmental metal pollution is a common problem threatening sustainable and safe crop production. Heavy metals (HMs) cause toxicity by targeting key molecules and life processes in plant cells. Plants counteract excess metals in the environment by enhancing defense responses, such as metal chelation, isolation to vacuoles, regulating metal intake through transporters, and strengthening antioxidant mechanisms. In recent years, microRNAs (miRNAs), as a small non-coding RNA, have become the central regulator of a variety of abiotic stresses, including HMs. With the introduction of the latest technologies such as next-generation sequencing (NGS), more and more miRNAs have been widely recognized in several plants due to their diverse roles. Metal-regulated miRNAs and their target genes are part of a complex regulatory network. Known miRNAs coordinate plant responses to metal stress through antioxidant functions, root growth, hormone signals, transcription factors (TF), and metal transporters. This article reviews the research progress of miRNAs in the stress response of plants to the accumulation of HMs, such as Cu, Cd, Hg, Cr, and Al, and the toxicity of heavy metal ions.

Crosstalk and gene expression in microorganisms under metals stress

Contamination of the environment with heavy metals (HMs) has led to huge global environmental issues. Industrialization activities such as mining, manufacturing, and construction generate massive amounts of toxic waste, posing environmental risks. HMs soil pollution causes a variety of environmental issues and has a detrimental effect on both animals and plants. To remove HMs from the soil, traditional physico-chemical techniques such as immobilization, electro-remediation, stabilization, and chemical reduction are used. Moreover, the high energy, trained manpower, and hazardous chemicals required by these methods make them expensive and non-environmentally friendly. Bioremediation process, which involves microorganism-based and microorganism-associated-plant-based approaches, is an ecologically sound and cost-effective strategy for restoring HMs polluted soil. Microbes adjust their physiology to these conditions to live, which can involve significant variations in the expression of the genes. A set of genes are activated in response to toxic metals in microbes. They can also adapt by modifying their shape, fruiting bodies creating biofilms, filaments, or chemotactically migrating away from stress chemicals. Microbes including Bacillus sp., Pseudomonas sp., and Aspergillus sp. has been found to have high metals remediation and tolerance capacity of up to 98% whether isolated or in combination with plants like Helianthus annuus, Trifolium repens, and Vallisneria denseserrulata. Several of the regulatory systems that have been discovered are unique, but there is also a lot of "cross-talk" among networks. This review discusses the current state of knowledge regarding the microbial signaling responses, and the function of microbes in HMs stress resistance.

An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo

Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.

The Multiverse of Plant Small RNAs: How Can We Explore It?

Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.

Nanomaterials coupled with microRNAs for alleviating plant stress: a new opening towards sustainable agriculture

Plant growth and development is influenced by their continuous interaction with the environment. Their cellular machinery is geared to make rapid changes for adjusting the morphology and physiology to withstand the stressful changes in their surroundings. The present scenario of climate change has however intensified the occurrence and duration of stress and this is getting reflected in terms of yield loss. A number of breeding and molecular strategies are being adopted to enhance the performance of plants under abiotic stress conditions. In this context, the use of nanomaterials is gaining momentum. Nanotechnology is a versatile field and its application has been demonstrated in almost all the existing fields of science. In the agriculture sector, the use of nanoparticles is still limited, even though it has been found to increase germination and growth, enhance physiological and biochemical activities and impact gene expression. In this review, we have summarized the use and role of nanomaterial and small non-coding RNAs in crop improvement while highlighting the potential of nanomaterial assisted eco-friendly delivery of small non-coding RNAs as an innovative strategy for mitigating the effect of abiotic stress.

Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?

Contamination of the biosphere by heavy metals has been rising, due to accelerated anthropogenic activities, and is nowadays, a matter of serious global concern. Removal of such inorganic pollutants from aquatic environments via biological processes has earned great popularity, for its cost-effectiveness and high efficiency, compared to conventional physicochemical methods. Among candidate organisms, microalgae offer several competitive advantages; phycoremediation has even been claimed as the next generation of wastewater treatment technologies. Furthermore, integration of microalgae-mediated wastewater treatment and bioenergy production adds favorably to the economic feasibility of the former process-with energy security coming along with environmental sustainability. However, poor biomass productivity under abiotic stress conditions has hindered the large-scale deployment of microalgae. Recent advances encompassing molecular tools for genome editing, together with the advent of multiomics technologies and computational approaches, have permitted the design of tailor-made microalgal cell factories, which encompass multiple beneficial traits, while circumventing those associated with the bioaccumulation of unfavorable chemicals. Previous studies unfolded several routes through which genetic engineering-mediated improvements appear feasible (encompassing sequestration/uptake capacity and specificity for heavy metals); they can be categorized as metal transportation, chelation, or biotransformation, with regulation of metal- and oxidative stress response, as well as cell surface engineering playing a crucial role therein. This review covers the state-of-the-art metal stress mitigation mechanisms prevalent in microalgae, and discusses putative and tested metabolic engineering approaches, aimed at further improvement of those biological processes. Finally, current research gaps and future prospects arising from use of transgenic microalgae for heavy metal phycoremediation are reviewed.

Plant RNA-mediated gene regulatory network

Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.

Recent advances in physiological and molecular mechanisms of heavy metal accumulation in plants

Among abiotic stress, the toxicity of metals impacts negatively on plants' growth and productivity. This toxicity promotes various perturbations in plants at different levels. To withstand stress, plants involve efficient mechanisms through the implication of various signaling pathways. These pathways enhance the expression of many target genes among them gene coding for metal transporters. Various metal transporters which are localized at the plasma membrane and/or at the tonoplast are crucial in metal stress response. Furthermore, metal detoxification is provided by metal-binding proteins like phytochelatins and metallothioneins. The understanding of the molecular basis of metal toxicities signaling pathways and tolerance mechanisms is crucial for genetic engineering to produce transgenic plants that enhance phytoremediation. This review presents an overview of the recent advances in our understanding of metal stress response. Firstly, we described the effect of metal stress on plants. Then, we highlight the mechanisms involved in metal detoxification and the importance of the regulation in the response to heavy metal stress. Finally, we mentioned the importance of genetic engineering for enhancing the phytoremediation technique. In the end, the response to heavy metal stress is complex and implicates various components. Thus, further studies are needed to better understand the mechanisms involved in response to this abiotic stress.

microRNA 166: an evolutionarily conserved stress biomarker in land plants targeting HD-ZIP family

MicroRNAs (miRNAs) are significant class of noncoding RNAs having analytical investigating and modulatory roles in various signaling mechanisms in plants related to growth, development and environmental stress. Conserved miRNAs are an affirmation of land plants evolution and adaptation. They are a proof of indispensable roles of endogenous gene modulators that mediate plant survival on land. Out of such conserved miRNA families, is one core miRNA known as miR166 that is highly conserved among land plants. This particular miRNA is known to primarily target HD ZIP-III transcription factors. miR166 has roles in various developmental processes, as well as regulatory roles against biotic and abiotic stresses in major crop plants. Major developmental roles indirectly modulated by miR166 include shoot apical meristem and vascular differentiation, leaf and root development. In terms of abiotic stress, it has decisive regulatory roles under drought, salinity, and temperature along with biotic stress management. miR166 and its target genes are also known for their beneficial synergy with microorganisms in leguminous crops in relation to lateral roots and nodule development. Hence it is important to study the roles of miR166 in different crop plants to understand its defensive roles against environmental stresses and improve plant productivity by reprogramming several gene functions at molecular levels. This review is hence a summary of different regulatory roles of miR166 with its target HD-ZIP III and its modulatory and fine tuning against different environmental stresses in various plants.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.

A regulatory network driving shoot lignification in rapidly growing bamboo

Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.

Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development

Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.

MicroRNAs: Tiny, powerful players of metal stress responses in plants

Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms

Heavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal-contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, that is uptake, transport, signaling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signaling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels, and the activation of mitogen-activated protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non-enzymatic antioxidants, such as ascorbate, metalloids, and even metal-binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signaling, and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Background

Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues.

Results

We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data.

Conclusions

To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07735-7.

Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance

Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.

The TAZ domain-containing proteins play important role in the heavy metals stress biology in plants

TAZ (transcriptional coactivator with PDZ-binding) zinc finger domains, also known as transcription adaptor putative zinc finger domains, that control diverse function in plant growth and development. Here, in the present study, we evaluated the role of the TAZ domain-containing gene in response to various heavy metals. Initially, we found a total of 3, 7, 8, 9, 9, 9, 7, 14, 6, 10, and 6 proteins containing TAZ domain in stiff brome, millet, sorghum, potato, pepper, maize, rice, apple, peach, pear, and tomato genome that could trigger the plant resistance against various heavy metals, respectively. Various in-silico approaches were applied such as duplication, phylogenetic analysis, and gene structure, to understand the basic features of the TAZ domain-containing genes in plants. Gene expression analyses were also performed under heavy metals (Cr, Zn, Ni, Cd, Co, Fe, Mn, and Pb). The results of quantitative real-time PCR analysis indicated that the TAZ gene family members were differentially expressed under different heavy metals. We further characterized the functions of the TAZ domain-containing gene under the heavy metal stresses by overexpressing the OsTAZ4 gene in Arabidopsis. The TAZ genes could promote plant resistance against various heavy metals by interacting with OsMYB34 and OsFHA9 transcription factors. The results will contribute to elucidate the relationship of TAZ proteins with heavy metals stresses and also ascertain the biological function in plant growth and development.

Confirmatory assays for transient changes of omics in soil invertebrates - Copper materials in a multigenerational exposure

Environmental risk assessment (ERA) based on effects caused by chronic and longer term exposure is highly relevant. Further, if mechanistic based approaches (e.g. omics) can be included, beyond apical endpoints (e.g. reproduction), the prediction of effects increases. For Cu NMs (and CuCl₂) this has been studied in detail, covering multi-omics and apical effects using the soil standard species Enchytraeus crypticus. The intermediate level effects like cell/tissue and organ alterations represent a missing link. In the present study we aimed to: 1) perform long term exposure to Cu materials (full life cycle and multigeneration, 46 and 224 days) to collect samples; 2) perform histology and immunohistochemistry on collected samples at 12 time points and 17 treatments; 3) integrate all levels of biological organization onto an adverse outcome pathway (AOP) framework. CuO NMs and CuCl₂ caused both similar and different stress response, either at molecular initiating events (MIE) or key events (KEs) of higher level of biological organization. Cell/Tissue and organ level, post-transcriptional and transcriptional mechanisms, through histone modifications and microRNA related protein, were similarly affected. While both Cu forms affected the Notch signalling pathway, CuCl₂ also caused oxidative stress. Different mechanisms of DNA methylation (epigenetics) were activated by CuO NMs and CuCl₂ at the MIE.

Epigenetic influence of environmentally neurotoxic metals

Continuous globalization and industrialization have ensured metals are an increasing aspect of daily life. Their usefulness in manufacturing has made them vital to national commerce, security and global economy. However, excess exposure to metals, particularly as a result of environmental contamination or occupational exposures, has been detrimental to overall health. Excess exposure to several metals is considered environmental risk in the aetiology of several neurological and neurodegenerative diseases. Metal-induced neurotoxicity has been a major health concern globally with intensive research to unravel the mechanisms associated with it. Recently, greater focus has been directed at epigenetics to better characterize the underlying mechanisms of metal-induced neurotoxicity. Epigenetic changes are those modifications on the DNA that can turn genes on or off without altering the DNA sequence. This review discusses how epigenetic changes such as DNA methylation, post translational histone modification and noncoding RNA-mediated gene silencing mediate the neurotoxic effects of several metals, focusing on manganese, arsenic, nickel, cadmium, lead, and mercury.

Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica

Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857–3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance.

•

Total of 44 Plant homeo-domain (PHD) finger proteins were identified & classified into 10 groups in Oryza sativa Indica.

•

This is the first report showing 5 newly identified putative miRNAs targeting three OsPHD genes i.e., OsPHD2, 11 and 35.

•

Expression analysis of PHD finger genes showed up-regulation of the 2 genes OsPHD 6 & 12 under salinity stress treatment.

•

Protein-protein network of OsPHDs showed protein partners that are involved in plant growth and abiotic stress tolerance.

A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease

MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24-72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.

In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress

Several biotic (bacterial and viral pathogenesis) and abiotic stress factors like salt, drought, cold, and extreme temperatures significantly reduce crop productivity and grain quality throughout the world. MicroRNAs (miRNAs) are small (~22 nucleotides) non-coding endogenous RNA molecules which negatively regulate gene expression at the post-transcriptional level either by degrading the target protein-coding mRNA genes or suppressing translation in plants. Dirigent (DIR) gene protein plays a crucial role as they are involved to dictate the stereochemistry of a compound synthesized by other enzymes as well as in lignifications against biotic and abiotic stress. In plants, several miRNAs, as well as their targets, are known to regulate stress response but systematic identification of the same is limited. The present work has been designed for in silico identification of miRNAs against a total of sixty-one DIR genes in Oryza sativa Indica followed by target prediction of identified miRNAs through the computational approach and thereafter validation of potential miRNAs in rice genotypes. We systematically identified 3 miRNA and their respective DIR specific target gene in Oryza sativa Indica. The expression of these three miRNAs and their respective DIR specific targets were validated in rice seedlings subjected to five different abiotic stress conditions (heavy metal, high temperature, low temperature, salinity and drought) by quantitative Real-Time PCR (qRT-PCR). Expression analysis indicated that miRNA under stress conditions regulates the gene expression of the DIR gene in rice. To the best of our knowledge this is this is the first report in any organism showing the expression of ath-miRf10317-akr, and osamiRf10761-akr miRNAs in response to various abiotic stresses.

•

Total 61 DIR proteins were identified & classified into 6 groups based on phylogeny analysis in Oryza sativa Indica.

•

Three miRNAs ath-miRf10317-akr, cre-miR910 and osa-miRf10761-akr were identified via computational approach.

•

These 3 miRNAs in response to abiotic stresses showed inverse expression pattern in the respective target genes.

•

This is the first report on expression of ath-miRf10317-akr, and osa-miRf10761-akr miRNAs in response to abiotic stresses.

Effects of sewage sludge supplementation on heavy metal accumulation and the expression of ABC transporters in Sinapis alba L. during assisted phytoremediation of contaminated sites

ATP binding cassette (ABC) transporters, types C, G, and B were monitored via qPCR in order to investigate the influence of heavy metal (HM) contamination of post-industrial and post-agricultural soils and the effects of its supplementation with sewage sludge, on Sinapis alba plants. Five house-keeping genes were selected and validated to ensure the best reference points. The relative expression of ABC types C and G genes was profoundly affected by experimental conditions and included their upregulation after plants exposure to heavy metals and downregulation after supplementation with sewage sludge. However, ABC type C was more responsive then type G. The experimental conditions altered the expression of ABC type C gene faster than ABC type G and thus, the expression of ABC type C can therefore potentially be used as a bioindicator during assisted phytoremediation of degraded sites. In clean soil, supplementation with sewage sludge with a slight content of heavy metals still caused an upregulation in the expression of ABC types C and G, which showed that proper toxicity assessments are necessary to ensure safe application of sewage sludge into soils. Results showed that the analysed genes take a significant part in plants metal detoxification and that their expression is regulated at transcriptional level after exposure to soil contaminated with heavy metals by both, industrial activities and by sewage sludge supplementation. Thus, their expression can potentially be used as an early-warning biomarker when soil supplementation with sewage sludge is incorporated into the soil-management process.

Genome-wide analysis of laccase genes in moso bamboo highlights PeLAC10 involved in lignin biosynthesis and in response to abiotic stresses

Twenty-three PeLACs have been identified in moso bamboo, overexpression of PeLAC10 increases the lignin content and confers drought and phenolic acid tolerance in transgenic Arabidopsis. Laccases (LACs) have multifunction involved in the processes of cell elongation, lignification and stress response in plants. However, the function of laccases in bamboo remain unclear. Here, a total of 23 laccase genes (PeLAC1-PeLAC23) were identified in moso bamboo (Phyllostachys edulis). The diverse gene structure and expression pattern of PeLACs suggested that their function should be spatiotemporal and complicated, which was supported by the expression profiles in different tissues of moso bamboo. Eighteen PeLACs were identified as the targets of ped-miR397. The putative ped-miR397-binding site in the coding region of PeLAC10 was further confirmed by RLM-5' RACE, indicating that PeLAC10 was regulated by ped-miR397 after transcription. With the increasing shoot height, the expression abundance of PeLAC10 was up-regulated and reached the maximum in 15 cm shoots, while that of ped-miR397 was relative lower and showed the minimum in 15 cm shoots. PeLAC10 was up-regulated obviously under both ABA (100 μmol L^-1) and NaCl (400 mmol L^-1) treatments, and it was down-regulated under the GA₃ (100 μmol L^-1) treatment. The transgenic Arabidopsis plants over-expressing PeLAC10 became slightly smaller and their petioles were shorter than those of Col-0. However, they had a stronger capacity in resistance to phenolic acids and drought besides higher lignin content in stems. These results indicated that overexpression of PeLAC10 was helpful to increase the content of lignin in transgenic Arabidopsis and improve the adaptability to phenolic acid and drought stresses.

The Effects of Cadmium Toxicity

Cadmium (Cd) is a toxic non-essential transition metal that poses a health risk for both humans and animals. It is naturally occurring in the environment as a pollutant that is derived from agricultural and industrial sources. Exposure to cadmium primarily occurs through the ingestion of contaminated food and water and, to a significant extent, through inhalation and cigarette smoking. Cadmium accumulates in plants and animals with a long half-life of about 25-30 years. Epidemiological data suggest that occupational and environmental cadmium exposure may be related to various types of cancer, including breast, lung, prostate, nasopharynx, pancreas, and kidney cancers. It has been also demonstrated that environmental cadmium may be a risk factor for osteoporosis. The liver and kidneys are extremely sensitive to cadmium's toxic effects. This may be due to the ability of these tissues to synthesize metallothioneins (MT), which are Cd-inducible proteins that protect the cell by tightly binding the toxic cadmium ions. The oxidative stress induced by this xenobiotic may be one of the mechanisms responsible for several liver and kidney diseases. Mitochondria damage is highly plausible given that these organelles play a crucial role in the formation of ROS (reactive oxygen species) and are known to be among the key intracellular targets for cadmium. When mitochondria become dysfunctional after exposure to Cd, they produce less energy (ATP) and more ROS. Recent studies show that cadmium induces various epigenetic changes in mammalian cells, both in vivo and in vitro, causing pathogenic risks and the development of various types of cancers. The epigenetics present themselves as chemical modifications of DNA and histones that alter the chromatin without changing the sequence of the DNA nucleotide. DNA methyltransferase, histone acetyltransferase, histone deacetylase and histone methyltransferase, and micro RNA are involved in the epigenetic changes. Recently, investigations of the capability of sunflower (Helianthus annuus L.), Indian mustard (Brassica juncea), and river red gum (Eucalyptus camaldulensis) to remove cadmium from polluted soil and water have been carried out. Moreover, nanoparticles of TiO2 and Al2O3 have been used to efficiently remove cadmium from wastewater and soil. Finally, microbial fermentation has been studied as a promising method for removing cadmium from food. This review provides an update on the effects of Cd exposure on human health, focusing on the cellular and molecular alterations involved.

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

Emerging Roles of microRNAs in Plant Heavy Metal Tolerance and Homeostasis

Heavy metal stress is a major growth- and yield-limiting factor for plants. Heavy metals include essential metals (copper, iron, zinc, and manganese) and non-essential metals (cadmium, mercury, aluminum, arsenic, and lead). Plants use complex mechanisms of gene regulation under heavy metal stress. MicroRNAs are 21-nucleotide non-coding small RNAs as important modulators of gene expression post-transcriptionally. Recently, high-throughput sequencing has led to the identification of an increasing number of heavy-metal-responsive microRNAs in plants. Metal-regulated microRNAs and their target genes are part of a complex regulatory network that controls various biological processes, including heavy metal uptake and transport, protein folding and assembly, metal chelation, scavenging of reactive oxygen species, hormone signaling, and microRNA biogenesis. In this review, we summarize the recent molecular studies that identify heavy-metal-regulated microRNAs and their roles in the regulation of target genes as part of the microRNA-associated regulatory network in response to heavy metal stress in plants.

MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower

Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.

Cadmium-Induced Renal Cell Toxicity Is Associated With MicroRNA Deregulation

Cadmium is an environmental pollutant well known for its nephrotoxic effects. Nevertheless, mechanisms underlying nephrotoxicity continue to be elucidated. MicroRNAs (miRNAs) have emerged in recent years as modulators of xenobiotic-induced toxicity. In this context, our study aimed at elucidating whether miRNAs are involved in renal proximal tubular toxicity induced by cadmium exposure. We showed that cadmium exposure, in 2 distinct renal proximal tubular cell models (renal proximal tubular epithelial cell [RPTEC]/human telomerase reverse transcriptase [hTERT] and human kidney-2), resulted in cytotoxicity associated with morphological changes, overexpression of renal injury markers, and induction of apoptosis and inflammation processes. Cadmium exposure also resulted in miRNA modulation, including the significant upregulation of 38 miRNAs in RPTEC/hTERT cells. Most of these miRNAs are known to target genes whose coding proteins are involved in oxidative stress, inflammation, and apoptosis, leading to tissue remodeling. In conclusion, this study provides a list of dysregulated miRNAs which may play a role in the pathophysiology of cadmium-induced kidney damages and highlights promising cadmium molecular biomarkers that warrants to be further evaluated.