Genome-wide analysis of plant metal transporters, with an emphasis on poplar

Molecular evolution and functional diversification of metal tolerance protein families in cereals plants and function of maize MTP protein

Plants employ metal tolerance proteins (MTPs) to confer tolerance by sequestering excess ions into vacuoles. MTPs belong to the cation diffusion facilitator (CDF) family, which facilitates the transport of divalent transition metal cations. In this study, we conducted a comprehensive analysis of the MTP gene families across 21 plant species, including maize (Zea mays). A total of 247 MTP genes were identified within these plant genomes and categorized into distinct subgroups, namely Zn-CDF, Mn-CDF, and Fe/Zn-CDF, based on phylogenetic analyses. This investigation encompassed the characterization of genomic distribution, gene structures, cis-regulatory elements, collinearity relationships, and gene ontology functions associated with MTPs. Transcriptomic analyses unveiled stress-specific expression patterns of MTP genes under various abiotic stresses. Moreover, quantitative RT-PCR assays were employed to assess maize MTP gene responses to diverse heavy metal stress conditions. Functional validation of metal tolerance roles was achieved through heterologous expression in yeast. This integrated evolutionary scrutiny of MTP families in cereals furnishes a valuable framework for the elucidation of MTP functions in subsequent studies. Notably, the prioritized MTP gene ZmMTP6 emerged as a positive regulator of plant Cd tolerance, thereby offering a pivotal genetic asset for the development of Cd-tolerant crops, particularly maize cultivars.

Recent advances in phyto-combined remediation of heavy metal pollution in soil

The global industrialization and modernization have witnessed a rapid progress made in agricultural production, along with the issue of soil heavy metal (HM) pollution, which has posed severe threats to soil quality, crop yield, and human health. Phytoremediation, as an alternative to physical and chemical methods, offers a more cost-effective, eco-friendly, and aesthetically appealing means for in-situ remediation. Despite its advantages, traditional phytoremediation faces challenges, including variable soil physicochemical properties, the bioavailability of HMs, and the slow growth and limited biomass of plants used for remediation. This study presents a critical overview of the predominant plant-based HM remediation strategies. It expounds upon the mechanisms of plant absorption, translocation, accumulation, and detoxification of HMs. Moreover, the advancements and practical applications of phyto-combined remediation strategies, such as the addition of exogenous substances, genetic modification of plants, enhancement by rhizosphere microorganisms, and intensification of agricultural technologies, are synthesized. In addition, this paper also emphasizes the economic and practical feasibility of some strategies, proposing solutions to extant challenges in traditional phytoremediation. It advocates for the development of cost-effective, minimally polluting, and biocompatible exogenous substances, along with the careful selection and application of hyperaccumulating plants. We further delineate specific future research avenues, such as refining genetic engineering techniques to avoid adverse impacts on plant growth and the ecosystem, and tailoring phyto-combined strategies to diverse soil types and HM pollutants. These proposed directions aim to enhance the practical application of phytoremediation and its integration into a broader remediation framework, thereby addressing the urgent need for sustainable soil decontamination and protection of ecological and human health.

Glomus versiforme and intercropping with Sphagneticola calendulacea decrease Cd accumulation in maize

Little information is available on the influence of the compound use of intercropping (IN) and arbuscular mycorrhizal fungus (AMF) on Cd accumulation and the expression of Cd transporter genes in two intercropped plants. A pot experiment was conducted to study the influences of IN and AMF-Glomus versiforme on growth and Cd uptake of two intercropped plants-maize and Cd hyperaccumulator Sphagneticola calendulacea, and the expression of Cd transporter genes in maize in Cd-polluted soils. IN, AMF and combined treatments of IN and AMF (IN + AMF) obviously improved biomass, photosynthesis and total antioxidant capacities of two plants. Moreover, single and compound treatments of IN and AMF evidently reduced Cd contents in maize, and the greatest decreases appeared in the compound treatment. However, Cd contents of S. calendulacea in IN, AMF and IN + AMF groups were notably improved. Furthermore, the single and compound treatments of IN and AMF significantly downregulated the expression levels of Nramp1, HMA1, ABCC1 and ABCC10 in roots and leaves, and the largest decreases were observed in the combined treatment. Our work first revealed that the combined use of IN and AMF appeared to have a synergistic effect on decreasing Cd content by downregulating the expression of Cd transporter genes in maize.

Mechanisms of low cadmium accumulation in crops: A comprehensive overview from rhizosphere soil to edible parts

Cadmium (Cd) is a toxic heavy metal often found in soil and agricultural products. Due to its high mobility, Cd poses a significant health risk when absorbed by crops, a crucial component of the human diet. This absorption primarily occurs through roots and leaves, leading to Cd accumulation in edible parts of the plant. Our research aimed to understand the mechanisms behind the reduced Cd accumulation in certain crop cultivars through an extensive review of the literature. Crops employ various strategies to limit Cd influx from the soil, including rhizosphere microbial fixation and altering root cell metabolism. Additional mechanisms include membrane efflux, specific transport, chelation, and detoxification, facilitated by metalloproteins such as the natural resistance-associated macrophage protein (Nramp) family, heavy metal P-type ATPases (HMA), zinc-iron permease (ZIP), and ATP-binding cassette (ABC) transporters. This paper synthesizes differences in Cd accumulation among plant varieties, presents methods for identifying cultivars with low Cd accumulation, and explores the unique molecular biology of Cd accumulation. Overall, this review provides a comprehensive resource for managing agricultural lands with lower contamination levels and supports the development of crops engineered to accumulate minimal amounts of Cd.

Molecular characterization of genes involved in tolerance of cadmium in Triticum aestivum (L.) under Cd stress

The NRAMPs (natural resistance-associated macrophage proteins) are major transporters for the absorption and transport of metals like Pb, Zn, Mn, Fe, and Cd in plants. While NRAMP gene family members have been extensively studied as metal transporters in model and other plants, little information has been reported on their role in Triticum aestivum, particularly in response to Cd stress. Current study reported 13 NRAMP candidates in the genome of T. aestivum. Phylogenetic analysis divided these into three clades. Motif and gene structure study showed that members in the same clades shared the same location and pattern, which further supported the phylogenetic analysis. The analysis of cis-acting elements in promoter sequences of NRAMP genes in wheat identified stress-responsive transcription factor binding sites. Multiple sequence alignment identified the conservation of important residues. Based on RNA-seq and qRT-PCR analysis, Cd stress-responsive variations of TaNRAMP gene expression were reported. This study provides comprehensive data to understand the TaNRAMP gene family, its features, and its expression, which will be a helpful framework for functional research.

Floral Development on Vitis vinifera Is Associated with MADS-Box Transcription Factors through the Transcriptional Regulation of VviZIP3

Several grapevine (Vitis vinifera L.) cultivars show a tendency to develop parthenocarpic seedless grapes, affecting fruit yield and quality. This reproductive disorder originates in defective ovule fertilization due to a failure in pollen tube growth. Zinc (Zn) is a crucial trace element, playing a vital role in various physiological and metabolic processes. It is particularly essential for the healthy growth of flowers and fruits. Insufficient zinc has been suggested as a potential reason for issues in this development process. This microelement is taken up through a mechanism that involves transporters, including the ZRT-IRT-like protein (ZIP) gene family, associated with the influx of Zn into the cell. In grapevines, 20 genes for ZIP-type transporters have been described. In this study, we analyzed the expression pattern of VviZIP3 during flower development and employ transgenic methods to assess its transcriptional regulation. Furthermore, through computational examination of the promoter region, we identified two CArG boxes, recognized as responsive elements to MADS transcription factors. These factors play a key role in shaping various components of a flower, such as pollen. Our investigation of the VviZIP3 promoter confirms the functionality of these CArG boxes. Overall, our results suggest that the increased expression of VviZIP3 during flowering is likely under the influence of MADS transcription factors.

The Malus domestica metal tolerance protein MdMTP11.1 was involved in the detoxification of excess manganese in Arabidopsis thaliana

Ion homeostasis is maintained in plant cells by specialized transporters. However, functional studies on Mn transporters in apple trees have not been reported. MdMTP11.1, which encodes a putative Mn-MTP transporter in Malus domestica, was expressed highly in leaves and induced by Mn stress. Subcellular localization analysis of the MdMTP11.1-GFP fusion protein indicated that MdMTP11.1 was targeted to the Golgi. Meanwhile, overexpression of MdMTP11.1 in Arabidopsis thaliana conferred increased resistance to plants under toxic Mn levels, as evidenced by increased biomass of whole plant and length of primary root. Analysis of Mn bioaccumulation indicated that overexpression of MdMTP11.1 effectively reduced the content of Mn in every subcellular component and chemical forms when the plants were subjected with Mn stress. The majority of Mn of action were bound to cell wall and combined with un-dissolved phosphate. Besides, contents of malondialdehyde (MDA), proline and hydrogen peroxide (H2O2) were significantly lower, while content of chlorophyll and activities of CAT, SOD, POD and APX were significantly higher in MdMTP11.1-over-expressing plants compared with that in wild type plants under Mn stress. Taken together, these results suggest that MdMTP11.1 is a Mn specific transporter localized to the Golgi can maintain the phenotype, reduce the Mn accumulation and alleviate damage of oxidative stress, conferring the positive role of Mn tolerance.

Characteristics of cadmium accumulation and tolerance in apple plants grown in different soils

Cadmium (Cd) is a nonessential element and highly toxic to apple tree. However, Cd accumulation, translocation and tolerance in apple trees planted in different soils remain unknown. To investigate soil Cd bioavailability, plant Cd accumulation, physiological changes as well as gene expression patterns in apple trees grown in five different soils, 'Hanfu' apple seedlings were planted in orchard soils collected from Maliangou village (ML), Desheng village (DS), Xishan village (XS), Kaoshantun village (KS) and Qianertaizi village (QT), and subjected to 500 μM CdCl₂ for 70 d. Results showed that soils of ML and XS had higher content of organic matter (OM), clay and silt, and cation exchange capacity (CEC) but lower sand content than the other soils, thereby reduced Cd bioavailability, which could be reflected by lower concentrations and proportions of acid-soluble Cd but higher concentrations and proportions of reducible and oxidizable Cd. The plants grown in soils of ML and XS had relatively lower Cd accumulation levels and bio-concentration factors than those grown in the other soils. Excess Cd reduced plant biomass, root architecture, and chlorophyll content in all plants but to relatively lesser degree in those grown in soils of ML and XS. The plants grown in soils of ML, XS and QT had comparatively lower reactive oxygen species (ROS) content, less membrane lipid peroxidation, and higher antioxidant content and enzyme activity than those grown in soils of DS and KS. Transcript levels of genes regulating Cd uptake, transport and detoxification such as HA11, VHA4, ZIP6, IRT1, NAS1, MT2, MHX, MTP1, ABCC1, HMA4 and PCR2 displayed significant differences in roots of plants grown in different soils. These results indicate that soil types affect Cd accumulation and tolerance in apple plants, and plants grown in soils with higher OM content, CEC, clay and silt content and lower sand content suffer less Cd toxicity.

Heavy metals and arsenic stress in food crops: Elucidating antioxidative defense mechanisms in hyperaccumulators for food security, agricultural sustainability, and human health

The spread of heavy metal(loid)s at soil-food crop interfaces has become a threat to sustainable agricultural productivity, food security, and human health. The eco-toxic effects of heavy metals on food crops can be manifested through reactive oxygen species that have the potential to disturb seed germination, normal growth, photosynthesis, cellular metabolism, and homeostasis. This review provides a critical overview of stress tolerance mechanisms in food crops/hyperaccumulator plants against heavy metals and arsenic (HM-As). The HM-As antioxidative stress tolerance in food crops is associated with changes in metabolomics (physico-biochemical/lipidomics) and genomics (molecular level). Furthermore, HM-As stress tolerance can occur through plant-microbe, phytohormone, antioxidant, and signal molecule interactions. Information regarding the avoidance, tolerance, and stress resilience of HM-As should help pave the way to minimize food chain contamination, eco-toxicity, and health risks. Advanced biotechnological approaches (e.g., genome modification with CRISPR-Cas9 gene editing) in concert with traditional sustainable biological methods are useful options to develop 'pollution safe designer cultivars' with increased climate change resilience and public health risks mitigation. Further, the usage of HM-As tolerant hyperaccumulator biomass in biorefineries (e.g., environmental remediation, value added chemicals, and bioenergy) is advocated to realize the synergy between biotechnological research and socio-economic policy frameworks, which are inextricably linked with environmental sustainability. The biotechnological innovations, if directed toward 'cleaner climate smart phytotechnologies' and 'HM-As stress resilient food crops', should help open the new path to achieve sustainable development goals (SDGs) and a circular bioeconomy.

The Maillard reaction in traditional method sparkling wine

The Maillard reaction between sugars and amino acids, peptides, or proteins generates a myriad of aroma compounds through complex and multi-step reaction pathways. While the Maillard has been primarily studied in the context of thermally processed foods, Maillard-associated products including thiazoles, furans, and pyrazines have been identified in aged sparkling wines, with associated bready, roasted, and caramel aromas. Sparkling wines produced in the bottle-fermented traditional method (Méthode Champenoise) have been the primary focus of studies related to Maillard-associated compounds in sparkling wine, and these wines undergo two sequential fermentations, with the second taking place in the final wine bottle. Due to the low temperature (15 ± 3°C) and low pH (pH 3-4) conditions during production and aging, we conclude that Maillard interactions may not proceed past intermediate stages. Physicochemical factors that affect the Maillard reaction are considered in the context of sparkling wine, particularly related to pH-dependent reaction pathways and existing literature pertaining to low temperature and/or low pH Maillard activity. A focus on the origins and composition of precursor species (amino acids and sugars) in sparkling wines is presented, as well as the potential role of metal ions in accelerating the Maillard reaction. Understanding the contributions of individual physicochemical factors to the Maillard reaction in sparkling wine enables a clearer understanding of reaction pathways and sensory outcomes. Advancements in analytical techniques for monitoring the Maillard reaction are also described, and important areas of future research on this topic are identified.

PcNRAMP1 Enhances Cadmium Uptake and Accumulation in Populus × canescens

Poplars are proposed for the phytoremediation of heavy metal (HM) polluted soil. Characterization of genes involved in HM uptake and accumulation in poplars is crucial for improving the phytoremediation efficiency. Here, Natural Resistance-Associated Macrophage Protein 1 (NRAMP1) encoding a transporter involved in cadmium (Cd) uptake and transport was functionally characterized in Populus × canescens. Eight putative PcNRAMPs were identified in the poplar genome and most of them were primarily expressed in the roots. The expression of PcNRAMP1 was induced in Cd-exposed roots and it encoded a plasma membrane-localized protein. PcNRAMP1 showed transport activity for Cd²⁺ when expressed in yeast. The PcNRAMP1-overexpressed poplars enhanced net Cd²⁺ influxes by 39–52% in the roots and Cd accumulation by 25–29% in aerial parts compared to the wildtype (WT). However, Cd-induced biomass decreases were similar between the transgenics and WT. Further analysis displayed that the two amino acid residues of PcNRAMP1, i.e., M236 and P405, play pivotal roles in regulating its transport activity for Cd²⁺. These results suggest that PcNRAMP1 is a plasma membrane-localized transporter involved in Cd uptake and transporting Cd from the roots to aerial tissues, and that the conserved residues in PcNRAMP1 are essential for its Cd transport activity in poplars.

Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions

Transition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar suggested that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.

Genome-Wide Identification of Strawberry Metal Tolerance Proteins and Their Expression under Cadmium Toxicity

Metal tolerance proteins (MTPs) are divalent cation transporters, known to upkeep the mineral nutrition of plants and heavy metal transport at cell, tissue, or whole plant levels. However, information related to evolutionary relationships and biological functions of MTP genes in strawberry (Fragaria vesca L.) remain elusive. Herein, we identified 12 MTP genes from the strawberry genome and divided them into three main groups (i.e., Zn-MTP, Fe/Zn MTP, and Mn-MTP), which is similar to MTP grouping in Arabidopsis and rice. The strawberry MTPs (FvMTPs) are predicted to be localized in the vacuole, while open reading frame (ORF) length ranged from 1113 to 2589 bp with 370 to 862 amino acids, and possess 4 to 6 transmembrane domains (TMDs), except for FvMTP12 that possessed 16 TMDs. All the FvMTP genes had putative cation efflux and cation diffusion facilitator domains along with a zinc dimerization (ZT-dimer) domain in Mn-MTPs. The collinear analysis suggested their conservation between strawberry and Arabidopsis MTPs. Promoter analysis also demonstrated that some of them might possibly be regulated by hormones and abiotic stress factors. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis proposed that FvMTP genes are involved in cation transport and homeostasis. The expression analysis showed that FvMTP1, FvMTP1.1, and FvMTP4 were significantly induced in leaf samples, while FvMTP1.1 and FvMTP4 were significantly regulated in roots of cadmium (Cd)-treated strawberry plants during progressive stress duration. The findings of Cd accumulation depicted that Cd contents were significantly higher in root tissues than that of leaf tissues of strawberry. These results are indicative of their response during the specific duration in Cd detoxification, while further functional studies can accurately verify their specific role.

A review on bioremediation approach for heavy metal detoxification and accumulation in plants

Nowadays, the accumulation of toxic heavy metals in soil and water streams is considered a serious environmental problem that causes various harmful effects on plants and animals. Phytoremediation is an effective, green, and economical bioremediation approach by which the harmful heavy metals in the contaminated ecosystem can be detoxified and accumulated in the plant. Hyperaccumulators exude molecules called transporters that carry and translocate the heavy metals present in the soil to different plant parts. The hyperaccumulator plant genes can confine higher concentrations of toxic heavy metals in their tissues. The efficiency of phytoremediation relies on various parameters such as soil properties (pH and soil type), organic matters in soil, heavy metal type, nature of rhizosphere, characteristics of rhizosphere microflora, etc. The present review comprehensively discusses the toxicity effect of heavy metals on the environment and different phytoremediation mechanisms for the transport and accumulation of heavy metals from polluted soil. This review gave comprehensive insights into plants tolerance for the higher heavy metal concentration their responses for heavy metal accumulation and the different mechanisms involved for heavy metal tolerance. The current status and the characteristic features that need to be improved in the phytoremediation process are also reviewed in detail.

Impact of arbuscular mycorrhiza on maize P1B-ATPases gene expression and ionome in copper-contaminated soils

Arbuscular mycorrhizal (AM) fungi, symbionts of most land plants, increase plant fitness in metal contaminated soils. To further understand the mechanisms of metal tolerance in the AM symbiosis, the expression patterns of the maize Heavy Metal ATPase (HMA) family members and the ionomes of non-mycorrhizal and mycorrhizal plants grown under different Cu supplies were examined. Expression of ZmHMA5a and ZmHMA5b, whose encoded proteins were predicted to be localized at the plasma membrane, was up-regulated by Cu in non-mycorrhizal roots and to a lower extent in mycorrhizal roots. Gene expression of the tonoplast ZmHMA3a and ZmHMA4 isoforms was up-regulated by Cu-toxicity in shoots and roots of mycorrhizal plants. AM mitigates the changes induced by Cu toxicity on the maize ionome, specially at the highest Cu soil concentration. Altogether these data suggest that in Cu-contaminated soils, AM increases expression of the HMA genes putatively encoding proteins involved in Cu detoxification and balances mineral nutrient uptake improving the nutritional status of the maize plants.

Genome-Wide Identification and Expression Profile Reveal Potential Roles of Peanut ZIP Family Genes in Zinc/Iron-Deficiency Tolerance

Zinc/iron-regulated transporter-like protein (ZIP) family genes play crucial roles in metal uptake and transport in plants. However, little is known about their functions in peanut. Here, genome-wide analysis identified 30 peanut AhZIP genes that were divided into four classes. Most AhZIPs experienced whole-genome or segmental duplication. AhZIP proteins harbored 3–8 transmembrane domains and a typical ZIP domain, showing considerable homology with BbZIP from Bordetella bronchiseptica. Clustered AhZIPs generally share similar gene/protein structures; however, unique features were found in AhIRT1.2, AhZIP1.2, AhZIP3.5 and AhZIP7.8. RNA-seq data revealed that AhZIP2.1/2.2, AhZIP4.1/4.2 and AhZIP11.1/11.2 were highly and preferentially expressed in roots, nodule and reproductive tissues. RT-qPCR analysis indicated that transcriptional responses of AhZIPs to Fe/Zn deficiency are cultivar dependent. The expressions of AhIRT1.1, AhIRT1.2 and AhZIP6.1 were closely related to Fe uptake and translocation. AhIRT1.1 and AhZIP7.2 expression were significantly correlated with Zn accumulation. The expression of AhIRT1.1, AhIRT1.2, AhZIP3.6, AhZIP6.1 and AhZIP11.1 was associated with Mn uptake and translocation. The results confirmed that AhZIP genes play crucial roles in the uptake and transport of Fe, Zn and Mn in peanut, providing clues to further functionally characterize AhZIP genes in the future.

The role of roots and rhizosphere in providing tolerance to toxic metals and metalloids

Human activity and natural processes have led to the widespread dissemination of metals and metalloids, many of which are toxic and have a negative impact on plant growth and development. Roots, as the first point of contact, are essential in endowing plants with tolerance to excess metal(loid) in the soil. The most important root processes that contribute to tolerance are: adaptation of transport processes that affect uptake efflux and long-distance transport of metal(loid)s; metal(loid) detoxification within root cells via conjugation to thiol rich compounds and subsequent sequestration in the vacuole; plasticity in root architecture; the presence of bacteria and fungi in the rhizosphere that impact on metal(loid) bioavailability; the role of root exudates. In this review, we provide details on these processes and assess their relevance on the detoxification of arsenic, cadmium, mercury and zinc in crops. Furthermore, we assess which of these strategies have been tested in field conditions and whether they are effective in terms of improving crop metal(loid) tolerance.

Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress

Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.

Employing gene chip technology for monitoring and assessing soil heavy metal pollution

Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.

Comparative and Systematic Omics Revealed Low Cd Accumulation of Potato StMTP9 in Yeast: Suggesting a New Mechanism for Heavy Metal Detoxification

The metal tolerance protein (MTP) family is a very old family with evolutionary conservation and less specific amplification. It seems to retain the original functions of the ancestral genes and plays an important role in maintaining metal homeostasis in plant cells. We identified the potato MTP family members for the first time, the specific and conservative StMPTs were discovered by using systematic and comparative omics. To be surprised, members of the StMTP family seem to have mutated before the evolution of dicotyledon and monocotyledon, and even the loss of the entire subfamily (subfamily G6, G7). Interestingly, StMTP9 represents the conserved structure of the entire subfamily involved in toxic metal regulation. However, the gene structure and transmembrane domain of StMTP8 have undergone specific evolution, showing that the transmembrane domain (Motif13) located at the NH₂ terminal has been replaced by the signal peptide domain, so it was selected as the control gene of StMTP9. Through real-time fluorescence quantitative analysis of StMTPs under Cd and Zn stress, a co-expression network was constructed, and it was found that StMTP9 responded significantly to Cd stress, while StMTP8 did the opposite. What excites us is that by introducing StMTPs 8/9 into the ∆ycf1 yeast cadmium-sensitive mutant strain, the functional complementation experiment proved that StMTPs 8/9 can restore Cd tolerance. In particular, StMTP9 can greatly reduce the cadmium content in yeast cells, while StMTP8 cannot. These findings provide a reference for further research on the molecular mechanism of potato toxic metal accumulation.

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious as they contain health beneficial metabolites, vitamins, mineral elements and other nutrients. Excessive reliance on the mainstream staple crops has its own disadvantages. Traditional food plants are nowadays considered important crops of the future and can act as supplementary foods for the burgeoning global population. They can also act as emergency foods in situations such as COVID-19 and in times of other pandemics. The current situation necessitates locally available alternative nutritious TFPs for sustainable food production. To increase the cultivation or improve the traits in TFPs, it is essential to understand the molecular basis of the genes that regulate some important traits such as nutritional components and resilience to biotic and abiotic stresses. The integrated use of modern omics and gene editing technologies provide great opportunities to better understand the genetic and molecular basis of superior nutrient content, climate-resilient traits and adaptation to local agroclimatic zones. Recently, realizing the importance and benefits of TFPs, scientists have shown interest in the prospection and sequencing of TFPs for their improvements, cultivation and mainstreaming. Integrated omics such as genomics, transcriptomics, proteomics, metabolomics and ionomics are successfully used in plants and have provided a comprehensive understanding of gene-protein-metabolite networks. Combined use of omics and editing tools has led to successful editing of beneficial traits in several TFPs. This suggests that there is ample scope for improvement of TFPs for sustainable food production. In this article, we highlight the importance, scope and progress towards improvement of TFPs for valuable traits by integrated use of omics and gene editing techniques.

The transfer of trace metals in the soil-plant-arthropod system

Essential and non-essential trace metals are capable of causing toxicity to organisms above a threshold concentration. Extensive research has assessed the behaviour of trace metals in biological and ecological systems, but has typically focused on single organisms within a trophic level and not on multi-trophic transfer through terrestrial food chains. This reinforces the notion of metal toxicity as a closed system, failing to consider one trophic level as a pollution source to another; therefore, obscuring the full extent of ecosystem effects. Given the relatively few studies on trophic transfer of metals, this review has taken a compartment-based approach, where transfer of metals through trophic pathways is considered as a series of linked compartments (soil-plant-arthropod herbivore-arthropod predator). In particular, we consider the mechanisms by which trace metals are taken up by organisms, the forms and transformations that can occur within the organism and the consequences for trace metal availability to the next trophic level. The review focuses on four of the most prevalent metal cations in soil which are labile in terrestrial food chains: Cd, Cu, Zn and Ni. Current knowledge of the processes and mechanisms by which these metals are transformed and moved within and between trophic levels in the soil-plant-arthropod system are evaluated. We demonstrate that the key factors controlling the transfer of trace metals through the soil-plant-arthropod system are the form and location in which the metal occurs in the lower trophic level and the physiological mechanisms of each organism in regulating uptake, transformation, detoxification and transfer. The magnitude of transfer varies considerably depending on the trace metal concerned, as does its toxicity, and we conclude that biomagnification is not a general property of plant-arthropod and arthropod-arthropod systems. To deliver a more holistic assessment of ecosystem toxicity, integrated studies across ecosystem compartments are needed to identify critical pathways that can result in secondary toxicity across terrestrial food-chains.

An Overview of Morpho-Physiological, Biochemical, and Molecular Responses of Sorghum Towards Heavy Metal Stress

Heavy metal (HM) contamination is a serious global environmental crisis. Over the past decade, industrial effluents, modern agricultural practices, and other anthropogenic activities have significantly depleted the soil environment. In plants, metal toxicity leads to compromised growth, development, productivity, and yield. Also, HMs negatively affect human health due to food chain contamination. Thus, it is imperative to reduce metal accumulation and toxicity. In nature, certain plant species exhibit an inherent capacity of amassing large amounts of HMs with remarkable tolerance. These plants with unique characteristics can be employed for the remediation of contaminated soil and water. Among different plant species, Sorghum bicolor has the potential of accumulating huge amounts of HMs, thus could be regarded as a hyperaccumulator. This means that it is a metal tolerant, high biomass producing energy crop, and thus can be utilized for phytoremediation. However, high concentrations of HMs hamper plant height, root hair density, shoot biomass, number of leaves, chlorophyll, carotenoid, and carbohydrate content. Thus, understanding the response of Sorghum towards different HMs holds considerable importance. Considering this, we have uncovered the basic information about the metal uptake, translocation, and accumulation in Sorghum. Plants respond to different HMs via sensing, signaling, and modulations in physico-chemical processes. Therefore, in this review, a glimpse of HM toxicity and the response of Sorghum at the morphological, physiological, biochemical, and molecular levels has been provided. The review highlights the future research needs and emphasizes the extensive molecular dissection of Sorghum to explore its genetic adaptability towards different abiotic stresses that can be exploited to develop resilient crop varieties.

The Role of Aquaporin Overexpression in the Modulation of Transcription of Heavy Metal Transporters under Cadmium Treatment in Poplar

Populus alba ‘Villafranca’ clone is well-known for its tolerance to cadmium (Cd). To determine the mechanisms of Cd tolerance of this species, wild-type (wt) plants were compared with transgenic plants over-expressing an aquaporin (aqua1, GenBank GQ918138). Plants were maintained in hydroponic conditions with Hoagland’s solution and treated with 10 µM of Cd, renewed every 5 d. The transcription levels of heavy metal transporter genes (PaHMA2, PaNRAMP1.3, PaNRAMP2, PaNRAMP3.1, PaNRAMP3.2, PaABCC9, and PaABCC13) were analyzed at 1, 7, and 60 d of treatment. Cd application did not induce visible toxicity symptoms in wt and aqua1 plants even after 2 months of treatment confirming the high tolerance of this poplar species to Cd. Most of the analyzed genes showed in wt plants a quick response in transcription at 1 d of treatment and an adaptation at 60 d. On the contrary, a lower transcriptional response was observed in aqua1 plants in concomitance with a higher Cd concentration in medial leaves. Moreover, PaHMA2 showed at 1 d an opposite trend within organs since it was up-regulated in root and stem of wt plants and in leaves of aqua1 plants. In summary, aqua1 overexpression in poplar improved Cd translocation suggesting a lower Cd sensitivity of aqua1 plants. This different response might be due to a different transcription of PaNRAMP3 genes that were more transcribed in wt line because of the importance of this gene in Cd compartmentalization.

Leveraging computational genomics to understand the molecular basis of metal homeostasis

Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.

Endomembrane Reorganization Induced by Heavy Metals

Plant cells maintain plasmatic concentrations of essential heavy metal ions, such as iron, zinc, and copper, within the optimal functional range. To do so, several molecular mechanisms have to be committed to maintain concentrations of non-essential heavy metals and metalloids, such as cadmium, mercury and arsenic below their toxicity threshold levels. Compartmentalization is central to heavy metals homeostasis and secretory compartments, finely interconnected by traffic mechanisms, are determinant. Endomembrane reorganization can have unexpected effects on heavy metals tolerance altering in a complex way membrane permeability, storage, and detoxification ability beyond gene's expression regulation. The full understanding of endomembrane role is propaedeutic to the comprehension of translocation and hyper-accumulation mechanisms and their applicative employment. It is evident that further studies on dynamic localization of these and many more proteins may significantly contribute to the understanding of heavy metals tolerance mechanisms. The aim of this review is to provide an overview about the endomembrane alterations involved in heavy metals compartmentalization and tolerance in plants.

Multi-genomic analysis of the cation diffusion facilitator transporters from algae

Metal transport processes are relatively poorly understood in algae in comparison to higher plants and other eukaryotes. A screen of genomes from 33 taxonomically diverse algal species was conducted to identify members of the Cation Diffusion Facilitator (CDF) family of metal ion transporter. All algal genomes contained at least one CDF gene with four species having >10 CDF genes (median of 5 genes per genome), further confirming that this is a ubiquitous gene family. Phylogenetic analysis suggested a CDF gene organisation of five groups, which includes Zn-CDF, Fe/Zn-CDF and Mn-CDF groups, consistent with previous phylogenetic analyses, and two functionally undefined groups. One of these undefined groups was algal specific although excluded chlorophyte and rhodophyte sequences. The majority of sequences (22 out of 26 sequences) from this group had a putative ion binding site motif within transmembrane domain 2 and 5 that was distinct from other CDF proteins, such that alanine or serine replaced the conserved histidine residue. The phylogenetic grouping was supported by sequence cluster analysis. Yeast heterologous expression of CDF proteins from Chlamydomonas reinhardtii indicated Zn²⁺ and Co²⁺ transport function by CrMTP1, and Mn²⁺ transport function by CrMTP2, CrMTP3 and CrMTP4, which validated the phylogenetic prediction. However, the Mn-CDF protein CrMTP3 was also able to provide zinc and cobalt tolerance to the Zn- and Co-sensitive zrc1 cot1 yeast strain. There is wide diversity of CDF transporters within the algae lineage, and some of these genes may be attractive targets for future applications of metal content engineering in plants or microorganisms.

Drivers of Ectomycorrhizal Fungal Community Structure Associated with Pinus sylvestris var. mongolica Differ at Regional vs. Local Spatial Scales in Northern China

Pinus sylvestris var. mongolica, a widely planted tree species, is facing long-lasting, unresolved degradation in desertified Northern China. Ectomycorrhizal fungi (EMF) are closely related to the stand status, because they substantially participate in ecological processes of terrestrial forest ecosystems. EMF may be key to solving the introduction recession. Therefore, we performed DNA sequencing of P. sylvestris root samples from plantations and natural forests as control to characterize the EMF from semi-arid and dry sub-humid regions, using ITS Illumina sequencing and conventional soil physicochemical index determination. The results indicated that (1) the dominant EMF genera were Suillus, Rhizopogon, and Wilcoxina in the Hulunbuir, Mu Us, and Horqin Sandy Lands, respectively. Their dominance retained with stand ageing. (2) Plantation EM fungal diversity differs significantly among the three sandy lands and was significantly lower than in natural forest. The diversity varied with stand age, showing distinct trends at the local scale. (3) At the regional scale, the mean annual sunshine times and the soil organic carbon content affect EMF diversity. The community composition and structure were more characterized by temperature and precipitation. At the local scale, besides the soil organic carbon content, the EM fungal community composition and structure were correlated with total nitrogen and phosphorus content (Hulunbuir), the total phosphorus content (Mu Us), and the pH and total soil porosity (Horqin). The EM fungal community composition and structure have the obvious geographical distribution variation; they were strongly correlated with the meteorological elements and soil nutrients at the regional scale. At the local scale, they were jointly driven by stand age and soil properties. This improved information contributes to increasing the understanding of the interaction between EMF and forest ecosystems and guides sustainable forest management of degraded P. sylvestris plantations.

Genome-Wide Identification of Metal Tolerance Protein Genes in Populus trichocarpa and Their Roles in Response to Various Heavy Metal Stresses

Metal tolerance proteins (MTPs) are plant divalent cation transporters that play important roles in plant metal tolerance and homeostasis. Poplar is an ideal candidate for the phytoremediation of heavy metals because of its numerous beneficial attributes. However, the definitive phylogeny and heavy metal transport mechanisms of the MTP family in poplar remain unknown. Here, 22 MTP genes in P. trichocarpa were identified and classified into three major clusters and seven groups according to phylogenetic relationships. An evolutionary analysis suggested that PtrMTP genes had undergone gene expansion through tandem or segmental duplication events. Moreover, all PtrMTPs were predicted to localize in the vacuole and/or cell membrane, and contained typical structural features of the MTP family, cation efflux domain. The temporal and spatial expression pattern analysis results indicated the involvement of PtrMTP genes in poplar developmental control. Under heavy metal stress, most of PtrMTP genes were induced by at least two metal ions in roots, stems or leaves. In addition, PtrMTP8.1, PtrMTP9 and PtrMTP10.4 displayed the ability of Mn transport in yeast cells, and PtrMTP6 could transport Co, Fe and Mn. These findings will provide an important foundation to elucidate the biological functions of PtrMTP genes, and especially their role in regulating heavy metal tolerance in poplar.

Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes

Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.

Poplar rotation coppice at a trace element-contaminated phytomanagement site: A 10-year study revealing biomass production, element export and impact on extractable elements

Growing lignocellulosic crops on marginal lands could compose a substantial proportion of future energy resources. The potential of poplar was explored, by devising a field trial of two hectares in 2007 in a metal-contaminated site to quantify the genotypic variation in the growth traits of 14 poplar genotypes grown in short-rotation coppice and to assess element transfer and export by individual genotypes. Our data led us to conclusions about the genotypic variations in poplar growth on a moderately contaminated site, with the Vesten genotype being the most productive. This genotype also accumulated the least amounts of trace elements, whereas the Trichobel genotype accumulated up to 170 mg Zn kg^-1 DW in the branches, with large variation being exhibited among the genotypes for trace element (TE) accumulation. Soil element depletion occurred for a range of TEs, whereas the soil content of major nutrients and the pH remained unchanged or slightly increased after 10 years of poplar growth. The higher TE content of bark tissues compared with the wood and the higher proportion of bark in branches compared with the wood led us to recommend that only stem wood be harvested, instead of the whole tree, which will enable a reduction in the risks encountered with TE-enriched biomass in the valorization process.

Effects of Exogenous Organic Acids on Cd Tolerance Mechanism of Salix variegata Franch. Under Cd Stress

Chelate induction of organic acids has been recognized to enhance metal uptake and translocation in plants, but the underlying mechanism remains unclear. In this study, seedlings of Salix variegata were hydroponically exposed to the combinations of Cd (0 and 50 μM) and three exogenous organic acids (100 μM of citric, tartaric, or malic acid). Plant biomass, antioxidant enzymes, non-protein thiol compounds (NPT) content, and the expression of candidate genes associated with Cd accumulation and tolerance were determined. Results showed that Cd significantly inhibited plant biomass but stimulated the activity of antioxidant enzymes in the roots and leaves, while the lipid peroxidation increased as well. Respective addition of three organic acids greatly enhanced plant resistance to oxidative stress and reduced the lipid peroxidation induced by Cd, with the effect of malic acid showing greatest. The addition of organic acids also significantly increased the content of glutathione in the root, further improving the antioxidant capacity and potential of phytochelatin biosynthesis. Moreover, Cd induced the expression level of candidate genes in roots of S. variegata. The addition of three organic acids not only promoted the expression of candidate genes but also drastically increased Cd accumulation in S. variegata. In summary, application of citric, tartaric, or malic acid alleviated Cd-imposed toxicity through the boost of enzymatic and non-enzymatic antioxidants and candidate gene expression, while their effects on Cd tolerance and accumulation of S. variegata differed.

Transcriptome Analysis of Wheat Roots Reveals a Differential Regulation of Stress Responses Related to Arbuscular Mycorrhizal Fungi and Soil Disturbance

Symbioses with soil microorganisms are central in shaping the diversity and productivity of land plants and provide protection against a diversity of stresses, including metal toxicity. Arbuscular mycorrhizal fungi (AMF) can form extensive extraradical mycelial networks (ERM), which are very efficient in colonizing a new host. We quantified the responses of transcriptomes of wheat and one AMF partner, Rhizoglomus irregulare, to soil disturbance (Undisturbed vs. Disturbed) and to two different preceding mycotrophic species (Ornithopus compressus and Lolium rigidum). Soil disturbance and preceding plant species engender different AMF communities in wheat roots, resulting in a differential tolerance to soil manganese (Mn) toxicity. Soil disturbance negatively impacted wheat growth under manganese toxicity, probably due to the disruption of the ERM, and activated a large number of stress and starvation-related genes. The O. compressus treatment, which induces a greater Mn protection in wheat than L. rigidum, activated processes related to cellular division and growth, and very few related to stress. The L. rigidum treatment mostly induced genes that were related to oxidative stress, disease protection, and metal ion binding. R. irregulare cell division and molecular exchange between nucleus and cytoplasm were increased by O. compressus. These findings are highly relevant for sustainable agricultural systems, when considering a fit-for-purpose symbiosis.

Physiological and molecular mechanisms of heavy metal accumulation in nonmycorrhizal versus mycorrhizal plants

Uptake, translocation, detoxification, and sequestration of heavy metals (HMs) are key processes in plants to deal with excess amounts of HM. Under natural conditions, plant roots often establish ecto- and/or arbuscular-mycorrhizae with their fungal partners, thereby altering HM accumulation in host plants. This review considers the progress in understanding the physiological and molecular mechanisms involved in HM accumulation in nonmycorrhizal versus mycorrhizal plants. In nonmycorrhizal plants, HM ions in the cells can be detoxified with the aid of several chelators. Furthermore, HMs can be sequestered in cell walls, vacuoles, and the Golgi apparatus of plants. The uptake and translocation of HMs are mediated by members of ZIPs, NRAMPs, and HMAs, and HM detoxification and sequestration are mainly modulated by members of ABCs and MTPs in nonmycorrhizal plants. Mycorrhizal-induced changes in HM accumulation in plants are mainly due to HM sequestration by fungal partners and improvements in the nutritional and antioxidative status of host plants. Furthermore, mycorrhizal fungi can trigger the differential expression of genes involved in HM accumulation in both partners. Understanding the molecular mechanisms that underlie HM accumulation in mycorrhizal plants is crucial for the utilization of fungi and their host plants to remediate HM-contaminated soils.

Divergent biology of facultative heavy metal plants

Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current literature favours the idea that hyperaccumulation of heavy metals serves plants as deterrent against attack by feeding animals (termed elemental defense hypothesis). The capability to hyperaccumulate heavy metals in A. halleri and N. caerulescens is achieved by duplications and alterations of the cis-regulatory properties of genes coding for heavy metal transporting/excreting proteins. Several metallophytes have developed ecotypes with a varying content of such heavy metal transporters as an adaption to the specific toxicity of a heavy metal site.

Exogenous glutathione enhances cadmium accumulation and alleviates its toxicity in Populus × canescens

Glutathione (GSH) plays an important role in cadmium (Cd) tolerance in woody plants, but the underlying mechanisms remain largely unknown. To elucidate the physiological and transcriptional regulation mechanisms of GSH-mediated Cd tolerance in woody plants, we exposed Populus × canescens (Ait.) Smith saplings to either 0 or 75 μM Cd together with one of three external GSH levels. Glutathione treatments include buthionine sulfoximine (BSO, an inhibitor of GSH biosynthesis), no external GSH and exogenous GSH. External GSH resulted in higher Cd2+ uptake rate in the roots, greater Cd amount in poplars, lower Cd-induced H2O2 levels in the roots, and higher contents of endogenous GSH in Cd-treated roots and leaves. Furthermore, external GSH led to upregulated transcript levels of several genes including zinc/iron regulated transporter related protein 6.2 (ZIP6.2) and natural resistance-associated macrophage protein 1.3 (NRAMP1.3), which probably take part in Cd uptake, glutathione synthetase 2 (GS2) implicated in Cd detoxification, metal tolerance protein 1 (MTP1) and ATP-binding cassette transporter C3 (ABCC3) involved in Cd vacuolar accumulation in the roots, γ-glutamylcysteine synthetase (ECS) and phytochelatin synthetase family protein 1 (PCS1) involved in Cd detoxification, and oligopeptide transporter 7 (OPT7) probably implicated in Cd detoxification in the leaves of Cd-exposed P. × canescens. In contrast, BSO often displayed the opposite effects on Cd-triggered physiological and transcriptional regulation responses in poplars. These results suggest that exogenous GSH can enhance Cd accumulation and alleviate its toxicity in poplars. This is probably attributed to external-GSH-induced higher net Cd2+ influx in the roots, greater Cd accumulation in aerial parts, stronger scavenging of reactive oxygen species, and transcriptional overexpression of several genes involved in Cd uptake, detoxification and accumulation.

Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus

Ionic aluminum (Al) in acidic soils, comprising approximately 50% of arable land globally, is highly toxic to most plant species. Populus grow naturally in acidic soils and tolerate high concentrations of Al. Multidrug and toxic compound extrusion (MATE) family genes in plants are involved in responses to Al tolerance. To date, however, the functional roles of the MATE genes in Populus remain unclear. In the present study, 71 putative MATE transporters were predicted in the genome of Populus trichocarpa. The chromosome distribution, phylogenetic relationships, and expression level analysis revealed that four candidate MATE genes belonging to subgroup IIIc might contribute to high Al tolerance in poplar. Further, the expression levels of two subgroup IIIc members, PtrMATE1 and PtrMATE2, were induced by Al stress. Transient expression in onion epidermal cells showed that PtrMATE1 was localized to the plasma membrane. Overexpression of PtrMATE1 increased Al-induced secretion of citrate from the root apex of transgenic plants. Al-induced inhibition of root growths were alleviated in both PtrMATE1 overexpression lines in Populus and in Arabidopsis compared with wild-type plants. In addition, PtrMATE1 expression was induced at 12 h after exposure to Al stress whereas PtrMATE2 expression was induced at 24 h, indicating that these proteins coordinately function in response to Al stress in poplar. Taken together, these results provide important insights into the molecular mechanisms involved in Al tolerance in poplar.

The SlZRT1 Gene Encodes a Plasma Membrane-Located ZIP (Zrt-, Irt-Like Protein) Transporter in the Ectomycorrhizal Fungus Suillus luteus

Zinc (Zn) is an essential micronutrient but may become toxic when present in excess. In Zn-contaminated environments, trees can be protected from Zn toxicity by their root-associated micro-organisms, in particular ectomycorrhizal fungi. The mechanisms of cellular Zn homeostasis in ectomycorrhizal fungi and their contribution to the host tree's Zn status are however not yet fully understood. The aim of this study was to identify and characterize transporters involved in Zn uptake in the ectomycorrhizal fungus Suillus luteus, a cosmopolitan pine mycobiont. Zn uptake in fungi is known to be predominantly governed by members of the ZIP (Zrt/IrtT-like protein) family of Zn transporters. Four ZIP transporter encoding genes were identified in the S. luteus genome. By in silico and phylogenetic analysis, one of these proteins, SlZRT1, was predicted to be a plasma membrane located Zn importer. Heterologous expression in yeast confirmed the predicted function and localization of the protein. A gene expression analysis via RT-qPCR was performed in S. luteus to establish whether SlZRT1 expression is affected by external Zn concentrations. SlZRT1 transcripts accumulated almost immediately, though transiently upon growth in the absence of Zn. Exposure to elevated concentrations of Zn resulted in a significant reduction of SlZRT1 transcripts within the first hour after initiation of the exposure. Altogether, the data support a role as cellular Zn importer for SlZRT1 and indicate a key role in cellular Zn uptake of S. luteus. Further research is needed to understand the eventual contribution of SlZRT1 to the Zn status of the host plant.

Genome-wide transcriptome profiling of genes associated with arsenate toxicity in an arsenic-tolerant rice mutant

The presence of arsenic (As) in polluted environments, such as ground water, affects the accumulation of As in rice grains and causes a serious threat to human health. However, the precise molecular regulations related to As toxicity and tolerance in rice remain largely unknown. In the present study, we developed an arsenic-tolerant type 1 (ATT1) rice mutant by γ-irradiation mutagenesis and performed genome-wide transcriptome analysis for the characterization of As-responsive genes. Toxicity inhibited transcriptional regulation of putative genes involved in photosynthesis, mitochondrial electron transport, and lipid biosynthesis metabolism in wild-type (WT) and ATT1 rice mutant. However, many cysteine biosynthesis-related genes were significantly upregulated in both plants. We also attempted to elucidate the putative genes associated with As tolerance by comparing transcriptomes and identified ATT1-specific transcriptional regulation of genes involved in stress and RNA-protein synthesis. This analysis identified 50 genes that had DNA polymorphisms in upstream regions that differed from those in the exon regions, which suggested that genetic variations in the upstream regions might enhance As tolerance in the mutants. Therefore, the expression profiles of the genes evaluated in this study may improve understanding of the functional roles of As-related genes in response to As tolerance mechanisms and could potentially be used in molecular breeding to limit As accumulation in rice grains.

Sedum alfredii SaNramp6 Metal Transporter Contributes to Cadmium Accumulation in Transgenic Arabidopsis thaliana

The plant natural resistance-associated macrophage protein (Nramp) family plays an important role in tolerance to heavy metal stress. However, few Nramps have been functionally characterized in the heavy metal-accumulating plant Sedum alfredii. Here, Nramp6 was cloned and identified from S. alfredii and its function analyzed in transgenic Arabidopsis thaliana. SaNramp6 cDNA contains an open reading frame of 1, 638 bp encoding 545 amino acids. SaNramp6's expression can be induced by cadmium (Cd) stress, and, after treatment, it peaked at one week and 12 h in the roots and leaves, respectively. SaNramp6 localized to the plasma membrane in protoplasts isolated from A. thaliana, Nicotiana benthamiana lower leaf and onion (Allium cepa) epidermal cells. The heterologous expression of SaNramp6 in the Δycf1 yeast mutant increased the Cd content in yeast cells. SaNramp6 also rescued the low Cd accumulation of the A. thaliana nramp1 mutant. Transgenic A. thaliana expressing SaNramp6 exhibited high Cd accumulation levels, as determined by a statistical analysis of the Cd concentration, translocation factors and net Cd²⁺ fluxes under Cd stress. Thus, SaNramp6 may play a significant role in improving Cd accumulation, and the gene may be useful for the biotechnological development of transgenic plants for phytoremediation.

Paxillus involutus-Facilitated Cd2+ Influx through Plasma Membrane Ca2+-Permeable Channels Is Stimulated by H2O2 and H+-ATPase in Ectomycorrhizal Populus × canescens under Cadmium Stress

Using a Non-invasive Micro-test Technique, flux profiles of Cd2+, Ca2+, and H+ were investigated in axenically grown cultures of two strains of Paxillus involutus (MAJ and NAU), ectomycorrhizae formed by these fungi with the woody Cd2+-hyperaccumulator, Populus × canescens, and non-mycorrhizal (NM) roots. The influx of Cd2+ increased in fungal mycelia, NM and ectomycorrhizal (EM) roots upon a 40-min shock, after short-term (ST, 24 h), or long-term (LT, 7 days) exposure to a hydroponic environment of 50 μM CdCl2. Cd2+ treatments (shock, ST, and LT) decreased Ca2+ influx in NM and EM roots but led to an enhanced influx of Ca2+ in axenically grown EM cultures of the two P. involutus isolates. The susceptibility of Cd2+ flux to typical Ca2+ channel blockers (LaCl3, GdCl3, verapamil, and TEA) in fungal mycelia and poplar roots indicated that the Cd2+ entry occurred mainly through Ca2+-permeable channels in the plasma membrane (PM). Cd2+ treatment resulted in H2O2 production. H2O2 exposure accelerated the entry of Cd2+ and Ca2+ in NM and EM roots. Cd2+ further stimulated H+ pumping activity benefiting NM and EM roots to maintain an acidic environment, which favored the entry of Cd2+ across the PM. A scavenger of reactive oxygen species, DMTU, and an inhibitor of PM H+-ATPase, orthovanadate, decreased Ca2+ and Cd2+ influx in NM and EM roots, suggesting that the entry of Cd2+ through Ca2+-permeable channels is stimulated by H2O2 and H+ pumps. Compared to NM roots, EM roots exhibited higher Cd2+-fluxes under shock, ST, and LT Cd2+ treatments. We conclude that ectomycorrhizal P. × canescens roots retained a pronounced H2O2 production and a high H+-pumping activity, which activated PM Ca2+ channels and thus facilitated a high influx of Cd2+ under Cd2+ stress.

Sexual competition affects biomass partitioning, carbon-nutrient balance, Cd allocation and ultrastructure of Populus cathayana females and males exposed to Cd stress

Although increasing attention has been paid to plant adaptation to soil heavy metal contamination, competition and neighbor effects have been largely overlooked, especially in dioecious plants. In this study, we investigated growth as well as biochemical and ultrastructural responses of Populus cathayana Rehder females and males to cadmium (Cd) stress under different sexual competition patterns. The results showed that competition significantly affects biomass partitioning, photosynthetic capacity, leaf and root ultrastructure, Cd accumulation, the contents of polyphenols, and structural and nonstructural carbohydrates. Compared with single-sex cultivation, plants of opposite sexes exposed to sexual competition accumulated more Cd in tissues and their growth was more strongly inhibited, indicating enhanced Cd toxicity under sexual competition. Under intrasexual competition, females showed greater Cd accumulation, more serious damage at the ultrastructural level and greater reduction in physiological activity than under intersexual competition, while males performed better under intrasexual competition than under intersexual competition. Males improved the female microenvironment by greater Cd uptake and lower resource consumption under intersexual competition. These results demonstrate that the sex of neighbor plants and competition affect sexual differences in growth and in key physiological processes under Cd stress. The asymmetry of sexual competition highlighted here might regulate population structure, and spatial segregation and phytoremediation potential of both sexes in P. cathayana growing in heavy metal-contaminated soils.

Improving prediction of metal uptake by Chinese cabbage (Brassica pekinensis L.) based on a soil-plant stepwise analysis

It is crucial to develop predictive soil-plant transfer (SPT) models to derive the threshold values of toxic metals in contaminated arable soils. The present study was designed to examine the heavy metal uptake pattern and to improve the prediction of metal uptake by Chinese cabbage grown in agricultural soils with multiple contamination by Cd, Cu, Ni, Pb, and Zn. Pot experiments were performed with 25 historically contaminated soils to determine metal accumulation in different parts of Chinese cabbage. Different soil bioavailable metal fractions were determined using different extractants (0.43M HNO3, 0.01M CaCl2, 0.005M DTPA, and 0.01M LWMOAs), soil moisture samplers, and diffusive gradients in thin films (DGT), and the fractions were compared with shoot metal uptake using both direct and stepwise multiple regression analysis. The stepwise approach significantly improved the prediction of metal uptake by cabbage over the direct approach. Strongly pH dependent or nonlinear relationships were found for the adsorption of root surfaces and in root-shoot uptake processes. Metals were linearly translocated from the root surface to the root. Therefore, the nonlinearity of uptake pattern is an important explanation for the inadequacy of the direct approach in some cases. The stepwise approach offers an alternative and robust method to study the pattern of metal uptake by Chinese cabbage (Brassica pekinensis L.).

Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra

Salix integra is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances in genomics for Salix are promising for future improvement in identification of new candidate genes involved in metal tolerance and accumulation. Thus, high-throughput transcriptome sequencing is essential for generating enormous transcript sequences from S. integra, especially for the purpose of Cd toxicity-responsive genes discovery. Using Illumina paired-end sequencing, approximately 60.05 million high-quality reads were obtained. De novo assembly yielded 80,105 unigenes with an average length of 703 bp, A total of 50,221 (63%) unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases. GO annotation reveals 1849 Cd responsive genes involving in Cd binding, transport, and detoxification and cellular Cd homeostasis, and these genes were highly enriched in plant response to Cd ion and Cd ion transport. By searching against the PlantCyc database, 509 unigenes were assigned to 14 PlantCyc pathways related to Cd transport and cellular detoxification, and many of them are genes encoding heavy metal ATPases (HMAs), nature resistance-associated with microphage proteins (NRAMPs), ATP-binding cassette (ABC) transporters, etc., Comprehensive RT-qPCR analysis of these selected genes in different tissues of S. integra under the control and Cd treatment revealed metallothionein-like protein (MT2A and MT2B), Metal tolerance protein (MTP1), ABCB25, NRAMP5, and ZIP1 may be involved in the Cd transport and detoxification in leaves, while NRAMP2, ZIP8, and NRAMP5 may be related to Cd transport in roots. Our study will enrich the sequence information of S. integra in public database, and would provide some new understanding of the molecular mechanisms of heavy metal tolerance and detoxification in willows.

Unraveling the role of dark septate endophyte (DSE) colonizing maize (Zea mays) under cadmium stress: physiological, cytological and genic aspects

A growing body of evidence suggests that plant root-associated fungi such as dark septate endophytes (DSE) can help plants overcome many biotic and abiotic stresses, of great interest is DSE-plant metal tolerance and alleviation capabilities on contaminated soils. However, the tolerance and alleviation mechanisms involved have not yet been elucidated. In the current study, the regulation and physiological response of Zea mays to its root-associated DSE, Exophiala pisciphila was analyzed under increased soil Cd stress (0, 10, 50, 100 mg kg⁻¹). Under Cd stress, DSE inoculation significantly enhanced the activities of antioxidant enzymes and low-molecular weight antioxidants, while also inducing increased Cd accumulation in the cell wall and conversion of Cd into inactive forms by shoot and root specific regulation of genes related to metal uptake, translocation and chelation. Our results showed that DSE colonization resulted in a marked tolerance to Cd, with a significant decrease in cadmium phytotoxicity and a significant increase in maize growth by triggering antioxidant systems, altering metal chemical forms into inactive Cd, and repartitioning subcellular Cd into the cell wall. These results provide comprehensive evidence for the mechanisms by which DSE colonization bioaugments Cd tolerance in maize at physiological, cytological and molecular levels.

Copper-transporting ATPases: The evolutionarily conserved machineries for balancing copper in living systems

Copper ATPases (Cu-ATPases) are ubiquitous transmembrane proteins using energy from ATP to transport copper across different biological membranes of prokaryotic and eukaryotic cells. As they belong to the P-ATPase family, Cu-ATPases contain a characteristic catalytic domain with an evolutionarily conserved aspartate residue phosphorylated by ATP to form a phosphoenzyme intermediate, as well as transmembrane helices containing a cation-binding cysteine-proline-cysteine/histidine/serine (CPx) motif for catalytic activation and cation translocation. In addition, most Cu-ATPases possess the N-terminal Cu-binding CxxC motif required for regulation of enzyme activity. In cells, the Cu-ATPases receive copper from soluble chaperones and maintain intracellular copper homeostasis by efflux of copper from the cell or transport of the metal into the intracellular compartments. In addition, copper pumps play an essential role in cuproprotein biosynthesis by the uptake of copper into the cell or delivery of the metal into the chloroplasts and thylakoid lumen or into the lumen of the secretory pathway, where the metal ion is incorporated into copper-dependent enzymes. In the recent years, significant progress has been made toward understanding the function and regulation of Cu-transporting ATPases in archaea, bacteria, yeast, humans, and plants, providing new insights into the specific physiological roles of these essential proteins in various organisms and revealing some conservative regulatory mechanisms of Cu-ATPase activity. In this review, the structural, biochemical, and functional properties of Cu-ATPases from phylogenetically different organisms are summarized and discussed, with particular attention given to the recent insights into the molecular biology of copper pumps in plants.

Identification of mutations allowing Natural Resistance Associated Macrophage Proteins (NRAMP) to discriminate against cadmium

Each essential transition metal plays a specific role in metabolic processes and has to be selectively transported. Living organisms need to discriminate between essential and non-essential metals such as cadmium (Cd(2+) ), which is highly toxic. However, transporters of the natural resistance-associated macrophage protein (NRAMP) family, which are involved in metal uptake and homeostasis, generally display poor selectivity towards divalent metal cations. In the present study we used a unique combination of yeast-based selection, electrophysiology on Xenopus oocytes and plant phenotyping to identify and characterize mutations that allow plant and mammalian NRAMP transporters to discriminate between their metal substrates. We took advantage of the increased Cd(2+) sensitivity of yeast expressing AtNRAMP4 to select mutations that decrease Cd(2+) sensitivity while maintaining the ability of AtNRAMP4 to transport Fe(2+) in a population of randomly mutagenized AtNRAMP4 cDNAs. The selection identified mutations in three residues. Among the selected mutations, several affect Zn(2+) transport, whereas only one, E401K, impairs Mn(2+) transport by AtNRAMP4. Introduction of the mutation F413I, located in a highly conserved domain, into the mammalian DMT1 transporter indicated that the importance of this residue in metal selectivity is conserved among NRAMP transporters from plant and animal kingdoms. Analyses of overexpressing plants showed that AtNRAMP4 affects the accumulation of metals in roots. Interestingly, the mutations selectively modify Cd(2+) and Zn(2+) accumulation without affecting Fe transport mediated by NRAMP4 in planta. This knowledge may be applicable for limiting Cd(2+) transport by other NRAMP transporters from animals or plants.