The development dynamics of the maize root transcriptome responsive to heavy metal Pb pollution

Integrative physiological, transcriptomic and metabolomic analysis reveals how the roots of two ornamental Hydrangea macrophylla cultivars cope with lead (Pb) toxicity

Lead (Pb) soil contamination has caused serious ecological and environmental issues. Hydrangea macrophylla is a potential Pb-contaminated soil remediation plant, however, their Pb stress defense mechanism is largely unknown. Here, the physiology, transcriptomic and metabolome of two H. macrophylla cultivars (ML, Pb-sensitive cultivar; JC, Pb-resistant cultivar) under Pb stress were investigated. The results demonstrated that JC performed superiorly, with activities of the antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were 1.25, 2.84, and 1.67 times higher than those of ML after Pb treatment, respectively, and the amount of soluble sugar in JC increased by 231.34 % compared with that in ML. The electrical conductivity (EC) value of the root exudates of JC was 43.71 % lower than that of ML under Pb stress. The non-targeted metabolomics analysis revealed 193 metabolites grouped into nine categories. Pb stress-induced differential expression of the 37 metabolites, among which the major metabolites up-regulated in ML were organic acids, while in JC, these were carbohydrates, fatty acids, organic acids and lipids. The transcriptomic analysis revealed that Pb exposure induced 1075 and 1314 differentially expressed genes (DEGs) in JC and ML, respectively. According to the functional annotation results, hub genes were primarily enriched in carbohydrate metabolism, root growth, and plant resistance to external stresses. A conjoint analysis of the two omics indicated that the cutin, suberine and wax biosynthesis pathway in JC played an essential role in Pb detoxification. These findings clarify the resistance mechanism of H. macrophylla to Pb stress and open up a new avenue for breeding H. macrophylla Pb-resistant cultivars.

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were "sulfur metabolism" and "glutathione metabolism", and the target pathways of NAP subfamily SiNACs were "ribosome" and "phenylpropanoid biosynthesis". This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize

Apetala2/ethylene response factor (AP2/ERF) is one of the largest families of transcription factors, regulating growth, development, and stress response in plants. Several studies have been conducted to clarify their roles in Arabidopsis and rice. However, less research has been carried out on maize. In this review, we systematically identified the AP2/ERFs in the maize genome and summarized the research progress related to AP2/ERF genes. The potential roles were predicted from rice homologs based on phylogenetic and collinear analysis. The putative regulatory interactions mediated by maize AP2/ERFs were discovered according to integrated data sources, implying that they involved complex networks in biological activities. This will facilitate the functional assignment of AP2/ERFs and their applications in breeding strategy.

Effects of ZmHIPP on lead tolerance in maize seedlings: Novel ideas for soil bioremediation

Extensive lead (Pb) absorption by plants affects their growth and development and causes damage to the human body by entering the food chain. In this study, we cloned ZmHIPP, a gene associated with Pb tolerance and accumulation in maize, using combined linkage mapping and weighted gene co-expression network analysis. We show that ZmHIPP, which encodes a heavy metal-associated isoprenylated plant protein, positively modulated Pb tolerance and accumulation in maize seedlings, Arabidopsis, and yeast. The genetic variation locus (A/G) in the promoter of ZmHIPP contributed to the phenotypic disparity in Pb tolerance among different maize inbred lines by altering the expression abundance of ZmHIPP. Knockdown of ZmHIPP significantly inhibited growth and decreased Pb accumulation in maize seedlings under Pb stress. ZmHIPP facilitated Pb deposition in the cell wall and prevented it from entering the intracellular organelles, thereby alleviating Pb toxicity in maize seedlings. Compared to that in the mutant zmhipp, the accumulated Pb in the wild-type line mainly consisted of the low-toxicity forms of Pb. Our study increases the understanding of the mechanism underlying Pb tolerance in maize and provides new insights into the bioremediation of Pb-polluted soil.

Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects

Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.

Characteristics of Cadmium and Lead Accumulation and Transfer by Chenopodium Quinoa Will

Potentially toxic elements are persistent in the environment and plants have the ability to absorb and transfer them from soil in edible parts. The objectives of this study were to characterize the distribution of Cd and Pb in quinoa tissues and to investigate their accumulation and transfer from irrigated water in edible parts of quinoa. For the purpose of this study experiment and simulated pollution in the form of different metal concentration in water that was used for irrigation was designed. Distribution of metals in quinoa were determined and analyzed in seed formation and maturation stage. Bioaccumulation and translocation factors were calculated to characterize the efficiency of quinoa to absorb metals. The results of our study indicated that quinoa adopts potentially toxic metals from substrate but does not accumulate them. The potential of such a conclusion is useful for exploring the use of quinoa as lead and cadmium excluders.

Transcriptome profiling of Fagopyrum tataricum leaves in response to lead stress

BACKGROUND

Lead (Pb) pollution is a widespread environmental problem that is harmful to living organisms. Tartary buckwheat (Fagopyrum tataricum), a member of the family Polygonaceae, exhibits short growth cycles and abundant biomass production, could be an ideal plant for phytoremediation due to its high Pb tolerance. Here, we aimed to explore the molecular basis underlying the responses of this plant to Pb stress.

RESULTS

In our study, ultrastructural localization assays revealed that Pb ions primarily accumulate in leaf vacuoles. RNA deep sequencing (RNA-Seq) of tartary buckwheat leaves was performed on two Pb-treated samples, named Pb1 (2000 mg/kg Pb (NO₃)₂) and Pb2 (10,000 mg/kg Pb (NO₃)₂), and a control (CK). A total of 88,977 assembled unigenes with 125,203,555 bases were obtained. In total, 2400 up-regulated and 3413 down-regulated differentially expressed genes (DEGs) were identified between CK and Pb1, and 2948 up-regulated DEGs and 3834 down-regulated DEGs were generated between CK and Pb2, respectively. Gene Ontology (GO) and pathway enrichment analyses showed that these DEGs were primarily associated with 'cell wall', 'binding', 'transport', and 'lipid and energy' metabolism. The results of quantitative real-time PCR (qRT-PCR) analyses of 15 randomly selected candidate DEGs and 6 regulated genes were consistent with the results of the transcriptome analysis. Heterologous expression assays in the yeast strain Δycf1 indicated that overexpressing CCCH-type zinc finger protein 14 (ZFP14) enhanced sensitivity to Pb²⁺, while 5 other genes, namely, metal transporter protein C2 (MTPC2), phytochelatin synthetase-like family protein (PCSL), vacuolar cation/proton exchanger 1a (VCE1a), natural resistance-associated macrophage protein 3 (Nramp3), and phytochelatin synthetase (PCS), enhanced the Pb tolerance of the mutant strain.

CONCLUSION

Combining our findings with those of previous studies, we generated a schematic model that shows the metabolic processes of tartary buckwheat under Pb stress. This study provides important data for further genomic analyses of the biological and molecular mechanisms of Pb tolerance and accumulation in tartary buckwheat.

Comparative Transcriptome Analysis of the Molecular Mechanism of the Hairy Roots of Brassica campestris L. in Response to Cadmium Stress

Brassica campestris L., a hyperaccumulator of cadmium (Cd), is considered a candidate plant for efficient phytoremediation. The hairy roots of Brassica campestris L are chosen here as a model plant system to investigate the response mechanism of Brassica campestris L. to Cd stress. High-throughput sequencing technology is used to identify genes related to Cd tolerance. A total of 2394 differentially expressed genes (DEGs) are identified by RNA-Seq analysis, among which 1564 genes are up-regulated, and 830 genes are down-regulated. Data from the gene ontology (GO) analysis indicate that DEGs are mainly involved in metabolic processes. Glutathione metabolism, in which glutathione synthetase and glutathione S-transferase are closely related to Cd stress, is identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A Western blot shows that glutathione synthetase and glutathione S-transferase are involved in Cd tolerance. These results provide a preliminary understanding of the Cd tolerance mechanism of Brassica campestris L. and are, hence, of particular importance to the future development of an efficient phytoremediation process based on hairy root cultures, genetic modification, and the subsequent regeneration of the whole plant.

Bioconcentration, Potential Health Risks, and a Receptor Prediction Model of Metal(loid)s in a Particular Agro-Ecological Area

To investigate the bioconcentration and potential health risks of metal(loid)s in a particular agro-ecological area, 230 pairs of soil and corresponding crop grain samples were collected from typical corn and wheat plants. The geo-accumulation index (Igeo), bioconcentration factors (BCF), health risk assessment (the target hazard quotient), and Receptor Prediction Model (PCS-SMLR) analysis were adopted to study the spatial distribution, assess the health risks, and predict the relationship between metal(loid)s and soil properties. It was found that the mean concentrations of Cu, Zn, Pb, Hg, and Cd in the study area’s agricultural soils exceeded the background soil concentrations, especially for Cd (0.2 mg/kg), Meanwhile, the corresponding Cd concentration in wheat samples was higher than the food quality limit. The results of the Igeo showed that the samples with a value higher than 0 for Cd and Hg accounted for 47.83% and 33.48%, respectively. The results of BCF of Cu, Zn, Cd, and As were higher in wheat than in corn, except for Ni. The target hazard quotient (TTHQ) of health risk of wheat, corn, and soil were higher for children (2.48) than adults (1.78), showing a potential health risk for individuals who mostly consume wheat. In addition, the PCS-SMLR analysis of the BCF prediction model for Cu, Zn, As, and soil properties showed differences in terms of the influences from wheat and corn. These results provide valuable information that not only can help local residents improve the staple food structure, but also can get provide a reference metal(loid)s concentration level for agricultural soils in the study area and restore a sustainable agro-ecological environment.

Transcription Factors Responding to Pb Stress in Maize

Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was used to analyse transcription factors (TFs) expressed under Pb stress based on RNA sequencing data. A total of 464 genes expressed in control check (CK) or Pb treatment samples were annotated as TFs. Among them, 262 differentially expressed transcription factors (DETs) were identified that responded to Pb treatment. Furthermore, the DETs were classified into 4 classes according to their expression patterns, and 17, 12 and 2 DETs were significantly annotated to plant hormone signal transduction, basal transcription factors and base excision repair, respectively. Seventeen DETs were found to participate in the plant hormone signal transduction pathway, where basic leucine zippers (bZIPs) were the most significantly enriched TFs, with 12 members involved. We further obtained 5 Arabidopsis transfer DNA (T-DNA) mutants for 6 of the maize bZIPs, among which the mutants atbzip20 and atbzip47, representing ZmbZIP54 and ZmbZIP107, showed obviously inhibited growth of roots and above-ground parts, compared with wild type. Five highly Pb-tolerant and 5 highly Pb-sensitive in maize lines were subjected to DNA polymorphism and expression level analysis of ZmbZIP54 and ZmbZIP107. The results suggested that differences in bZIPs expression partially accounted for the differences in Pb-tolerance among the maize lines. Our results contribute to the understanding of the molecular regulation mechanisms of TFs in maize under Pb stress.

Transcriptomic and physiological analyses of Medicago sativa L. roots in response to lead stress

Lead (Pb) is one of the nonessential and toxic metals that threaten the environment and human health. Medicago sativa L. is a legume with high salt tolerance and high biomass production. It is not only a globally important forage crop but is also an ideal plant for phytoremediation. However, the biological and molecular mechanisms that respond to heavy metals are still not well defined in M. sativa. In this study, de novo and strand-specific RNA-sequencing was performed to identify genes involved in the Pb stress response in M. sativa roots. A total of 415,350 unigenes were obtained from the assembled cDNA libraries, among which 5,416 were identified as significantly differentially expressed genes (DEGs) (false discovery rate < 0.005) between cDNA libraries from control and Pb-treated plants. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs showed they mainly clustered with terms associated with binding, transport, membranes, and the pathways related to signal and energy metabolism. Moreover, a number of candidate genes included antioxidant enzymes, metal transporters, and transcription factors involved in heavy metal response were upregulated under Pb stress. Quantitative real-time PCR(qRT-PCR) validation of the expression patterns of 10 randomly selected candidate DEGs were consistent with the transcriptome analysis results. Thus, this study offers new information towards the investigation of biological changes and molecular mechanisms related to Pb stress response in plants.

Transcriptome profilings of two tall fescue (Festuca arundinacea) cultivars in response to lead (Pb) stress

BACKGROUND

Lead (Pb) is one of the most toxic heavy metal environmental pollutants. Tall fescue is an important cold season turf grass which can tolerate and accumulate substantial amount of Pb. To estimate genes related to Pb response and the molecular mechanism associated with Pb tolerance and accumulation, we analyzed the transcriptome of tall fescue in response to Pb treatment.

RESULTS

RNA-sequencing was performed in two tall fescue cultivars, Pb tolerant Silverado and Pb sensitive AST7001. A total of 810,146 assembled unique transcripts representing 25,415 unigenes were obtained from the tall fescue leaves. Among the panel, 3,696 differentially expressed genes (DEGs) were detected between the Pb treated (1000 mg/L) and untreated samples. Gene ontology (GO) and pathway enrichment analysis demonstrated that the DEGs were mainly implicated in energy metabolism, metabolism of terpenoids and polyketides, and carbohydrate metabolism related pathways. The expression patterns of 16 randomly selected genes were in consistent with that from the Solexa analysis using quantitative reverse-transcription PCR. In addition, compared to the common transcriptional response to Pb stress in both cultivars, the regulation of numerous genes including those involved in zeatin biosynthesis, limonene and pinene degradation, phagosome was exclusive to one cultivar.

CONCLUSIONS

The tall fescue assembled transcriptome provided substantial molecular resources for further genomics analysis of turfgrass in response to heavy metal stress. The significant expression difference of specific unigenes may account for Pb tolerance or accumulation in two different tall fescue cultivars. This study provided new insights for the investigation of the molecular basis of Pb tolerance and accumulation in tall fescue as well as other related turf grass species.

Arbuscular Mycorrhizal Fungus Enhances Lateral Root Formation in Poncirus trifoliata (L.) as Revealed by RNA-Seq Analysis

Arbuscular mycorrhizal fungi (AMF) establish symbiosis with most terrestrial plants, and greatly regulate lateral root (LR) formation. Phosphorus (P), sugar, and plant hormones are proposed being involved in this regulation, however, no global evidence regarding these factors is available so far, especially in woody plants. In this study, we inoculated trifoliate orange seedlings (Poncirus trifoliata L. Raf) with an AMF isolate, Rhizophagus irregularis BGC JX04B. After 4 months of growth, LR formation was characterized, and sugar contents in roots were determined. RNA-Seq analysis was performed to obtain the transcriptomes of LR root tips from non-mycorrhizal and mycorrhizal seedlings. Quantitative real time PCR (qRT-PCR) of selected genes was also conducted for validation. The results showed that AMF significantly increased LR number, as well as plant biomass and shoot P concentration. The contents of glucose and fructose in primary root, and sucrose content in LR were also increased. A total of 909 differentially expressed genes (DEGs) were identified in response to AMF inoculation, and qRT-PCR validated the transcriptomic data. The numbers of DEGs related to P, sugar, and plant hormones were 31, 32, and 25, respectively. For P metabolism, the most up-regulated DEGs mainly encoded phosphate transporter, and the most down-regulated DEGs encoded acid phosphatase. For sugar metabolism, the most up-regulated DEGs encoded polygalacturonase and chitinase. For plant hormones, the most up-regulated DEGs were related to auxin signaling, and the most down-regulated DEGs were related to ethylene signaling. PLS-SEM analysis indicates that P metabolism was the most important pathway by which AMF regulates LR formation in this study. These data reveal the changes of genome-wide gene expression in responses to AMF inoculation in trifoliate orange and provide a solid basis for the future identification and characterization of key genes involved in LR formation induced by AMF.

OsARM1, an R2R3 MYB Transcription Factor, Is Involved in Regulation of the Response to Arsenic Stress in Rice

Bioaccumulation of arsenic (As) in rice (Oryza sativa) increases human exposure to this toxic, carcinogenic element. Recent studies identified several As transporters, but the regulation of these transporters remains unclear. Here, we show that the rice R2R3 MYB transcription factor OsARM1 (ARSENITE-RESPONSIVE MYB1) regulates As-associated transporters genes. Treatment with As(III) induced OsARM1 transcript accumulation and an OsARM1-GFP fusion localized to the nucleus. Histochemical analysis of OsARM1pro::GUS lines indicated that OsARM1 was expressed in the phloem of vascular bundles in basal and upper nodes. Knockout of OsARM1 (OsARM1-KO CRISPR/Cas9-generated mutants) improved tolerance to As(III) and overexpression of OsARM1 (OsARM1-OE lines) increased sensitivity to As(III). Measurement of As in As(III)-treated plants showed that under low As(III) conditions (2 μM), more As was transported from the roots to the shoots in OsARM1-KOs. By contrast, more As accumulated in the roots in OsARM1-OEs in response to high As(III) exposure (25 μM). In particular, the As(III) levels in node I were significantly higher in OsARM1-KOs, but significantly lower in OsARM1-OEs, compared to wild-type plants, implying that OsARM1 is important for the regulation of root-to-shoot translocation of As. Moreover, OsLsi1, OsLsi2, and OsLsi6, which encode key As transporters, were significantly downregulated in OsARM1-OEs and upregulated in OsARM1-KOs compared to wild type. Chromatin immunoprecipitation-quantitative PCR of OsARM1-OEs indicated that OsARM1 binds to the conserved MYB-binding sites in the promoters or genomic regions of OsLsi1, OsLsi2, and OsLsi6 in rice. Our findings suggest that the OsARM1 transcription factor has essential functions in regulating As uptake and root-to-shoot translocation in rice.