Variation in HMA4 gene copy number and expression among Noccaea caerulescens populations presenting different levels of Cd tolerance and accumulation

Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants

Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.

The response of physiological and xylem anatomical traits under cadmium stress in Pinus thunbergii seedlings

Studying the response of physiological and xylem anatomical traits under cadmium stress is helpful to understand plants' response to heavy metal stress. Here, seedlings of Pinus thunbergii Parl. were treated with 50, 100 and 150 mg kg-1 Cd2+ for 28 days. Cadmium and nonstructural carbohydrate content of leaves, stems and roots, root Cd2+ flux, cadmium distribution pattern in stem xylem and phloem, stem xylem hydraulic traits, cell wall component fractions of stems and roots, phytohormonal content such as abscisic acid, gibberellic acid 3, molecule -indole-3-acetic acid, and jasmonic acid from both leaves and roots, as well as xylem anatomical traits from both stems and roots were measured. Root Cd2+ flux increased from 50 to 100 mmol L-1 Cd2+ stress, however it decreased at 150 mmol L-1 Cd2+. Cellulose and hemicellulose in leaves, stems and roots did not change significantly under cadmium stress, while pectin decreased significantly. The nonstructural carbohydrate content of both leaves and stems showed significant changes under cadmium stress while the root nonstructural carbohydrate content was not affected. In both leaves and roots, the abscisic acid content significantly increased under cadmium stress, while the gibberellic acid 3, indole-3-acetic acid and jasmonic acid methylester content significantly decreased. Both xylem specific hydraulic conductivity and xylem water potential decreased with cadmium stress, however tracheid diameter and double wall thickness of the stems and roots were not affected. High cadmium intensity was found in both the stem xylem and phloem in all cadmium stressed treatments. Our study highlighted the in situ observation of cadmium distribution in both the xylem and phloem, and demonstrated the instant response of physiological traits such as xylem water potential, xylem specific hydraulic conductivity, root Cd2+ flux, nonstructural carbohydrate content, as well as phytohormonal content under cadmium stress, and the less affected traits such as xylem anatomical traits, cellulose and hemicellulose.

Divergent roles of IREG/Ferroportin transporters from the nickel hyperaccumulator Leucocroton havanensis

In response to our ever-increasing demand for metals, phytotechnologies are being developed to limit the environmental impact of conventional metal mining. However, the development of these technologies, which rely on plant species able to tolerate and accumulate metals, is partly limited by our lack of knowledge of the underlying molecular mechanisms. In this work, we aimed to better understand the role of metal transporters of the IRON REGULATED 1/FERROPORTIN (IREG/FPN) family from the nickel hyperaccumulator Leucocroton havanensis from the Euphorbiaceae family. Using transcriptomic data, we identified two homologous genes, LhavIREG1 and LhavIREG2, encoding divalent metal transporters of the IREG/FPN family. Both genes are expressed at similar levels in shoots, but LhavIREG1 shows higher expression in roots. The heterologous expression of these transporters in A. thaliana revealed that LhavIREG1 is localized to the plasma membrane, whereas LhavIREG2 is located on the vacuole. In addition, the expression of each gene induced a significant increase in nickel tolerance. Taken together, our data suggest that LhavIREG2 is involved in nickel sequestration in vacuoles of leaf cells, whereas LhavIREG1 is mainly involved in nickel translocation from roots to shoots, but could also be involved in metal sequestration in cell walls. Our results suggest that paralogous IREG/FPN transporters may play complementary roles in nickel hyperaccumulation in plants.

Significance and genetic control of membrane transporters to improve phytoremediation and biofortification processes

Humans frequently consume plant-based foods in their daily life. Contamination of agricultural soils by heavy metals (HMs) is a major food and nutritional security issue. The crop plants grown in HM-contaminated agricultural soil may accumulate more HMs in their edible part, further transferring into the food chain. Consumption of HM-rich crops can cause severe health issues in humans. On the other hand, the low content of the essential HM in the edible part of the crop also causes health problems. Therefore, researchers must try to reduce the non-essential HM in the edible part of the crop plants and improve the essential HMs. Phytoremediation and biofortification are the two strategies for resolving this problem. The genetic component helps to improve the efficiency of phytoremediation and biofortification processes in plants. They help eliminate HMs from soil and improve essential HM content in crop plants. The membrane transporter genes (genetic components) are critical in these two strategies. Therefore, engineering membrane transporter genes may help reduce the non-essential HM content in the edible part of crop plants. Targeted gene editing by genome editing tools like CRISPR could help plants achieve efficient phytoremediation and biofortification. This article covers gene editing's scope, application, and implication to improve the phytoremediation and biofortification processes in non-crop and crop plants.

Identification and functional analysis of calcium sensor calmodulins from heavy metal hyperaccumulator Noccaea caerulescens

Noccaea caerulescens (J. Presl & C. Presl) F. K. Mey. is a heavy metal hyperaccumulator exhibiting extreme tolerance to various environmental stresses. To date, the functional role of Ca2+ -binding protein in this plant is largely unknown. To investigate the function of calmodulins (CaMs) in N. caerulescens , CaM2 , a Ca2+ sensor encoding gene, was identified and functionally characterised. Protein structure analysis showed that NcCaM2 contains four classic exchange factor (EF)-hand motifs with high sequence similarity to the CaM proteins from model plant Arabidopsis thaliana L. Tissue specific expression analysis showed that NcCaM2 is constitutively expressed in stems, leaves, and roots. Expression level of NcCaM2 was significantly upregulated under various environmental stimulus, indicating a potential involvement of NcCaM2 in the tolerance to abiotic stresses. The heterologous expression of NcCaM2 in a yeast mutant strain increased the heavy metal tolerance in yeast cells. Furthermore, the constitutive expression of NcCaM2 enhanced the heavy metal tolerance capability of transgenic tobacco (Nicotiana tabacum L.) plants. Our data suggested an important role of NcCaM2 in the responses to environmental stresses and provided a potential target gene to enhance of the ability to hyperaccumulate metals.

Zinc- and nickel-induced changes in fatty acid profiles in the zinc hyperaccumulator Arabidopsis halleri and non-accumulator Arabidopsis lyrata

This pilot study aimed at comparing zinc (Zn) and nickel (Ni) effects on the fatty acid (FA) profiles, oxidative stress and desaturase activity in the Zn hyperaccumulator Arabidopsis halleri and the excluder Arabidopsis lyrata to allow a better picture of the physiological mechanisms which may contribute to metal tolerance or acclimation. The most significant changes in the FA composition were observed in the shoots of the hyperaccumulator and in the roots of the excluder, and were not only metal-dependent, but also species-specific, since the most significant changes in the shoots of A. halleri were observed under Ni treatment, though Ni, in contrast to Zn, was accumulated mainly in its roots. Several FAs appeared in the roots and shoots of A. lyrata only upon metal exposure, whereas they were already found in control A. halleri. In both species, there was an increase in oleic acid under Ni treatment in both organs, whereas in Zn-treated plants the increase was shown only for the shoots. A rare conjugated α-parinaric acid was identified only in the shoots of metal-treated A. halleri. In the shoots of the hyperaccumulator, there was an increase in the content of saturated FAs and a decrease in the content of unsaturated FAs, while in the roots of the excluder, the opposite pattern was observed. These metal-induced changes in FA composition in the shoots of A. halleri can lead to a decrease in the fluidity of membranes, which could diminish the penetration of ROS into the membrane and thus maintain its stability.

Microbe- plant interaction as a sustainable tool for mopping up heavy metal contaminated sites

BACKGROUND

Phytoremediation is a green technology that removes heavy metal (HM) contamination from the environment by using HM plant accumulators. Among soil microbiota, plant growth promoting bacteria (PGPR) have a role influencing the metal availability and uptake.

METHODS

This current study evaluates the plant growth promoting qualities of microbial flora isolated from rhizosphere, plant roots, and marine aquatic HMs polluted environments in Alexandria through several biochemical and molecular traits. Metal contents in both collected soils and plant tissues were measured. Transcript levels of marker genes (HMA3 and HMA4) were analyzed.

RESULTS

Three terrestrial and one aquatic site were included in this study based on the ICP-MS identification of four HMs (Zn, Cd, Cu, and Ni) or earlier reports of HMs contamination. Using the VITEK2 bacterial identification system, twenty-two bacteria isolated from these loci were biochemically described. Pseudomonas and Bacillus were the most dominant species. Furthermore, the soil microbiota collected from the most contaminated HMs site with these two were able to enhance the Helianthus annuus L. hyper-accumulation capacity significantly. Specifically, sunflower plants cultivated in soils with HMs adapted bacteria were able to accumulate about 1.7-2.5-folds more Zn and Cd in their shoots, respectively.

CONCLUSION

The influence of PGPR to stimulate crop growth under stress is considered an effective strategy. Overall, our findings showed that plants cultivated in HMs contaminated sites in the presence of PGPR were able to accumulate significant amounts of HMs in several plant parts than those cultivated in soils lacking microbiota.

Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation

Mineral nutrition is one of the key factors determining plant productivity. In plants, metal homeostasis is achieved through the functioning of a complex system governing metal uptake, translocation, distribution, and sequestration, leading to the maintenance of a regulated delivery of micronutrients to metal-requiring processes as well as detoxification of excess or non-essential metals. Low-molecular-weight ligands, such as nicotianamine, histidine, phytochelatins, phytosiderophores, and organic acids, play an important role in metal transport and detoxification in plants. Nicotianamine and histidine are also involved in metal hyperaccumulation, which determines the ability of some plant species to accumulate a large amount of metals in their shoots. In this review we extensively summarize and discuss the current knowledge of the main pathways for the biosynthesis of these ligands, their involvement in metal uptake, radial and long-distance transport, as well as metal influx, isolation and sequestration in plant tissues and cell compartments. It is analyzed how diverse endogenous ligand levels in plants can determine their different tolerance to metal toxic effects. This review focuses on recent advances in understanding the physiological role of these compounds in metal homeostasis, which is an essential task of modern ionomics and plant physiology. It is of key importance in studying the influence of metal deficiency or excess on various physiological processes, which is a prerequisite to the improvement of micronutrient uptake efficiency and crop productivity and to the development of a variety of applications in phytoremediation, phytomining, biofortification, and nutritional crop safety.

The Different Faces of Arabidopsis arenosa-A Plant Species for a Special Purpose

The following review article collects information on the plant species Arabidopsis arenosa. Thus far, A. arenosa has been known as a model species for autotetraploidy studies because, apart from diploid individuals, there are also tetraploid populations, which is a unique feature of this Arabidopsis species. In addition, A arenosa has often been reported in heavy metal-contaminated sites, where it occurs together with a closely related species A. halleri, a model plant hyperaccumulator of Cd and Zn. Recent studies have shown that several populations of A. arenosa also exhibit Cd and Zn hyperaccumulation. However, it is assumed that the mechanism of hyperaccumulation differs between these two Arabidopsis species. Nevertheless, this phenomenon is still not fully understood, and thorough research is needed. In this paper, we summarize the current state of knowledge regarding research on A. arenosa.

Current understanding of plant zinc homeostasis regulation mechanisms

The essential nature of Zn and widespread Zn deficiency in plants under field conditions underlie the great interest of researchers in the regulation of plant Zn homeostasis. Here, the current knowledge of plant Zn homeostasis regulation, mainly in A. thaliana, is reviewed. The plant Zn homeostasis machinery is regulated largely at the transcriptional level. Local regulation in response to changes in cellular Zn status is based on the transcription factors bZIP19 and bZIP23, which sense changes in free Zn²⁺ concentrations in the cell. However, there are likely other unidentified ways to sense cellular free Zn²⁺ concentrations in addition to the well-known bZIP19 and bZIP23 factors. In recent years, the existence of a shoot-derived systemic Zn deficiency signal, which is involved in the upregulation of Zn transport from roots to shoots, was demonstrated. Additionally, rates of mRNA degradation of Zn homeostasis genes are likely regulated by changes in cellular Zn status. In addition to the regulation of Zn transport, other mechanisms for the regulation of plant Zn homeostasis exist. "Zn sparing" mechanisms could be involved in the decrease in plant Zn requirements under Zn deficiency. Additionally, autophagy is probably regulated by local Zn status and involved in Zn reutilization at the cellular level. Current issues related to studying Zn homeostasis regulation are discussed.

Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations of Suillus brevipes

Gene copy number variation across individuals has been shown to track population structure and be a source of adaptive genetic variation with significant fitness impacts. In this study, we report opposite results for both predictions based on the analysis of gene copy number variants (CNVs) of Suillus brevipes, a mycorrhizal fungus adapted to coastal and montane habitats in California. In order to assess whether gene copy number variation mirrored population structure and selection in this species, we investigated two previously studied locally adapted populations showing a highly differentiated genomic region encompassing a gene predicted to confer salt tolerance. In addition, we examined whether copy number in the genes related to salt homeostasis was differentiated between the two populations. Although we found many instances of CNV regions across the genomes of S. brevipes individuals, we also found CNVs did not recover population structure and known salt-tolerance-related genes were not under selection across the coastal population. Our results contrast with predictions of CNVs matching single-nucleotide polymorphism divergence and showed CNVs of genes for salt homeostasis are not under selection in S. brevipes.

Evolution of the metal hyperaccumulation and hypertolerance traits

To succeed in life, living organisms have to adapt to the environmental issues to which they are subjected. Some plants, defined as hyperaccumulators, have adapted to metalliferous environments, acquiring the ability to tolerate and accommodate high amounts of toxic metal into their shoot, without showing symptoms of toxicity. The determinants for these traits and their mode of action have long been the subject of research, whose attention lately moved to the evolution of the hypertolerance and hyperaccumulation traits. Genetic evidence indicates that the evolution of both traits includes significant evolutionary events that result in species-wide tolerant and accumulating backgrounds. Different edaphic environments are responsible for subsequent refinement, by local adaptive processes, leading to specific strategies and various degrees of hypertolerance and hyperaccumulation, which characterize metallicolous from non-metallicolous ecotypes belonging to the same genetic unit. In this review, we overview the most updated concepts regarding the evolution of hyperaccumulation and hypertolerance, highlighting also the ecological context concerning the plant populations displaying this fascinating phenomenon.

Spatially-resolved localization and chemical speciation of nickel and zinc in Noccaea tymphaea and Bornmuellera emarginata

Hyperaccumulator plants present the ideal model system for studying the physiological regulation of the essential (and potentially toxic) transition elements nickel and zinc. This study used synchrotron X-ray Fluorescence Microscopy (XFM) elemental imaging and spatially resolved X-ray Absorption Spectroscopy (XAS) to elucidate elemental localization and chemical speciation of nickel and zinc in the hyperaccumulators Noccaea tymphaea and Bornmuellera emarginata (synonym Leptoplax emarginata). The results show that in the leaves of N. tymphaea nickel and zinc have contrasting localization, and whereas nickel is present in vacuoles of epidermal cells, zinc occurs mainly in the mesophyll cells. In the seeds Ni and Zn are similarly localized and strongly enriched in the cotyledons in N. tymphaea. Nickel is strongly enriched in the tip of the radicle of B. emarginata. Noccaea tymphaea has an Fe-rich provascular strand network in the cotyledons of the seed. The chemical speciation of Ni in the seeds of N. tymphaea is unequivocally associated with carboxylic acids, whereas Zn is present as the phytate complex. The spatially resolved spectroscopy did not reveal any spatial variation in chemical speciation of Ni and Zn within the N. tymphaea seed. The dissimilar ecophysiological behaviour of Ni and Zn in N. tymphaea and B. emarginata raises questions about the evolution of hyperaccumulation in these species.

Biomolecular approaches to understanding metal tolerance and hyperaccumulation in plants

Trace metal elements are essential for plant growth but become toxic at high concentrations, while some non-essential elements, such as Cd and As, show toxicity even in traces.

Influence of edaphic conditions and nitrogen fertilizers on cadmium and zinc phytoextraction efficiency of Noccaea caerulescens

The success of cadmium phytoextraction operations with Noccaea caerulescens varies by a factor of 70 between sites of trials. However, soil factors driving the efficiency of cadmium (Cd) and zinc (Zn) phytoextraction are still poorly understood, as are the effects of nitrogen fertilizers. We studied biomass production and Cd and Zn uptake by two contrasting populations of N. caerulescens, Ganges (metallicolous) and Wilwerwiltz (non-metallicolous) grown in pots on a range of 24 field contaminated soils for 20 weeks. The addition of KNO₃ and NH₄NO₃ fertilizers was also tested. Using model averaging of multiple regression models, we show that the major drivers of N. caerulescens growth are physical soil factors such as organic matter and soil bulk density while trace metal accumulation mainly relies on soil Cd and Zn exchangeable concentrations. We confirm the negative effect of soil copper (Cu) on growth, even at exchangeable concentrations below 30 mg kg^-1, and therefore on uptake efficiency, while increasing soil lead (Pb) content was related to increased biomass probably due to a protective effect against soil pathogens. Finally, there is a small positive effect of nitrogen fertilization on biomass production only in soils with low initial nitrogen content (under 25 μg g^-1 NO₃^-), while above this value, the positive impact of initial nitrogen content is offset by lower shoot Cd and Zn concentrations. Our data bring substantial information regarding the physico-chemical properties to ensure N. caerulescens growth: a soil bulk density under 1.05 kg/dm³, organic matter above 7% and pH under 7.5. We show that phytoextraction efficiency is maximal for moderate soil contamination in Cd (2-10 mg kg^-1) and Zn (300-1000 mg kg^-1).

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.

Site-specific regulation of transcriptional responses to cadmium stress in the hyperaccumulator, Sedum alfredii: based on stem parenchymal and vascular cells

We compared the transcriptomes of parenchymal and vascular cells of Sedum alfredii stem under Cd stress to reveal gene regulatory networks underlying Cd hyperaccumulation. Cadmium (Cd) hyperaccumulation in plants is a complex biological process controlled by gene regulatory networks. Efficient transport through vascular systems and storage by parenchymal cells are vital for Cd hyperaccumulation in the Cd hyperaccumulator Sedum alfredii, but the genes involved are poorly understood. We investigated the spatial gene expression profiles of transport and storage sites in S. alfredii stem using laser-capture microdissection coupled with RNA sequencing. Gene expression patterns in response to Cd were distinct in vascular and parenchymal cells, indicating functional divisions that corresponded to Cd transportation and storage, respectively. In vascular cells, plasma membrane-related terms enriched a large number of differentially-expressed genes (DEGs) for foundational roles in Cd transportation. Parenchymal cells contained considerable DEGs specifically concentrated on vacuole-related terms associated with Cd sequestration and detoxification. In both cell types, DEGs were classified into different metabolic pathways in a similar way, indicating the role of Cd in activating a systemic stress signalling network where ATP-binding cassette transporters and Ca²⁺ signal pathways were probably involved. This study identified site-specific regulation of transcriptional responses to Cd stress in S. alfredii and analysed a collection of genes that possibly function in Cd transportation and detoxification, thus providing systemic information and direction for further investigation of Cd hyperaccumulation molecular mechanisms.

Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase

The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.

Transcriptional effects of cadmium on iron homeostasis differ in calamine accessions of Noccaea caerulescens

Calamine accessions of the zinc/cadmium/nickel hyperaccumulator, Noccaea caerulescens, exhibit striking variation in foliar cadmium accumulation in nature. The Ganges accession (GA) from Southern France displays foliar cadmium hyperaccumulation (>1000 μg g^-1 DW), whereas the accession La Calamine (LC) from Belgium, with similar local soil metal composition, does not (<100 μg g^-1 DW). All calamine accessions are cadmium hypertolerant. To find out the differences between LC and GA in their basic adaptation mechanisms, we bypassed the cadmium excluding phenotype of LC by exposing the plants to 50 μm cadmium in hydroponics, achieving equal cadmium accumulation in the shoots. The iron content increased in the roots of both accessions. GA exhibited significant decreases in manganese and zinc contents in the roots and shoots, approaching those in LC. Altogether 702 genes responded differently to cadmium exposure between the accessions, 157 and 545 in the roots and shoots, respectively. Cadmium-exposed LC showed a stress response and had decreased levels of a wide range of photosynthesis-related transcripts. GA showed less changes, mainly exhibiting an iron deficiency-like response. This included increased expression of genes encoding five iron deficiency-regulated bHLH transcription factors, ferric reduction oxidase FRO2, iron transporters IRT1 and OPT3, and nicotianamine synthase NAS1, and decreased expression of genes encoding ferritins and NEET (a NEET family iron-sulfur protein), which is possibly involved in iron transfer, distribution and/or management. The function of the IRT1 gene in the accessions was compared. We conclude that the major difference between the two accessions is in the way they cope with iron under cadmium exposure.

Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity

The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.

Mechanisms of selenium hyperaccumulation in plants: A survey of molecular, biochemical and ecological cues

BACKGROUND

Selenium (Se) is a micronutrient required for many life forms, but toxic at higher concentration. Plants do not have a Se requirement, but can benefit from Se via enhanced antioxidant activity. Some plant species can accumulate Se to concentrations above 0.1% of dry weight and seem to possess mechanisms that distinguish Se from its analog sulfur (S). Research on these so-called Se hyperaccumulators aims to identify key genes for this remarkable trait and to understand ecological implications.

SCOPE OF REVIEW

This review gives a broad overview of the current knowledge about Se uptake and metabolism in plants, with a special emphasis on hypothesized mechanisms of Se hyperaccumulation. The role of Se in plant defense responses and the associated ecological implications are discussed.

MAJOR CONCLUSIONS

Hyperaccumulators have enhanced expression of S transport and assimilation genes, and may possess transporters with higher specificity for selenate over sulfate. Genes involved in antioxidant reactions and biotic stress resistance are also upregulated. Key regulators in these processes appear to be the growth regulators jasmonic acid, salicylic acid and ethylene. Hyperaccumulation may have evolved owing to associated ecological benefits, particularly protection against pathogens and herbivores, and as a form of elemental allelopathy.

GENERAL SIGNIFICANCE

Understanding plant Se uptake and metabolism in hyperaccumulators has broad relevance for the environment, agriculture and human and animal nutrition and may help generate crops with selenate-specific uptake and high capacity to convert selenate to less toxic, anticarcinogenic, organic Se compounds.

Contrasting cadmium resistance strategies in two metallicolous populations of Arabidopsis halleri

While cadmium (Cd) tolerance is a constitutive trait in the Arabidopsis halleri species, Cd accumulation is highly variable. Recent adaptation to anthropogenic metal stress has occurred independently within the genetic units of A. halleri and the evolution of different mechanisms involved in Cd tolerance and accumulation has been suggested. To gain a better understanding of the mechanisms underlying Cd tolerance and accumulation in A. halleri, ionomic inductively coupled plasma mass spectrometry (ICP-MS), transcriptomic (RNA sequencing) and metabolomic (high-performance liquid chromatography-mass spectrometry) profiles were analysed in two A. halleri metallicolous populations from different genetic units (PL22 from Poland and I16 from Italy). The PL22 and I16 populations were both hypertolerant to Cd, but PL22 hyperaccumulated Cd while I16 behaved as an excluder both in situ and when grown hydroponically. The observed hyperaccumulator vs excluder behaviours were paralleled by large differences in the expression profiles of transporter genes. Flavonoid-related transcripts and metabolites were strikingly more abundant in PL22 than in I16 shoots. The role of novel A. halleri candidate genes possibly involved in Cd hyperaccumulation or exclusion was supported by the study of corresponding A. thaliana knockout mutants. Taken together, our results are suggestive of the evolution of divergent strategies for Cd uptake, transport and detoxification in different genetic units of A. halleri.

Elemental assessment of vegetation via portable X-ray fluorescence (PXRF) spectrometry

Elemental concentrations in vegetation are of critical importance, whether establishing plant essential element concentrations (toxicity vs. deficiency) or investigating deleterious elements (e.g., heavy metals) differentially extracted from the soil by plants. Traditionally, elemental analysis of vegetation has been facilitated by acid digestion followed by quantification via inductively coupled plasma (ICP) or atomic absorption (AA) spectroscopy. Previous studies have utilized portable X-ray fluorescence (PXRF) spectroscopy to quantify elements in soils, but few have evaluated the vegetation. In this study, a PXRF spectrometer was employed to scan 228 organic material samples (thatch, deciduous leaves, grasses, tree bark, and herbaceous plants) from smelter-impacted areas of Romania, as well as National Institute of Standards and Technology (NIST) certified reference materials, to demonstrate the application of PXRF for elemental determination in vegetation. Samples were scanned in three conditions: as received from the field (moist), oven dry (70 °C), and dried and powdered to pass a 2 mm sieve. Performance metrics of PXRF models relative to ICP atomic emission spectroscopy were developed to asses optimal scanning conditions. Thatch and bark samples showed the highest mean PXRF and ICP concentrations (e.g., Zn, Pb, Cd, Fe), with the exceptions of K and Cl. Validation statistics indicate that the stable validation predictive capacity of PXRF increased in the following order: oven dry intact < field moist < oven dried and powdered. Even under field moist conditions, PXRF could reasonably be used for the determination of Zn (coefficient of determination, R²_val 0.86; residual prediction deviation, RPD 2.72) and Cu (R²_val 0.77; RPD 2.12), while dried and powdered samples allowed for stable validation prediction of Pb (R²_val 0.90; RPD 3.29), Fe (R²_val 0.80; RPD 2.29), Cd (R²_val 0.75; RPD 2.07) and Cu (R²_val 0.98; RPD of 8.53). Summarily, PXRF was shown to be a useful approach for quickly assessing the elemental concentration in vegetation. Future PXRF/vegetation research should explore additional elements and investigate its usefulness in evaluating phytoremediation effectiveness.

AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 (HMA4) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation.

Influence of sulfate supply on selenium uptake dynamics and expression of sulfate/selenate transporters in selenium hyperaccumulator and nonhyperaccumulator Brassicaceae

Stanleya pinnata not only hyperaccumulates selenium (Se) to 0.5% of its dry weight, but also exhibits higher tissue Se-to-sulfur (S) ratios than other species and its surroundings. To investigate the mechanisms underlying this Se enrichment, we compared S. pinnata with the nonhyperaccumulators S. elata and Brassica juncea for selenate uptake in long- (9 d) and short-term (1 h) assays, using different concentrations of selenate and competitor sulfate. Different sulfate pre-treatments (0, 0.5, 5 mM, 3 d) were also tested for effects on selenate uptake and sulfate transporters' expression. Relative to nonhyperaccumulators, S. pinnata showed higher rates of root and shoot Se accumulation and less competitive inhibition by sulfate or by high-S pretreatment. The selenate uptake rate for S. pinnata (1 h) was three- to four-fold higher than for nonhyperaccumulators, and not significantly affected by 100-fold excess sulfate, which reduced selenate uptake by 100% in S. elata and 40% in B. juncea. Real-time reverse transcription PCR indicated constitutive upregulation in S. pinnata of sulfate transporters SULTR1;2 (root influx) and SULTR2;1 (translocation), but reduced SULTR1;1 expression (root influx). In S. pinnata, selenate uptake and translocation rates are constitutively elevated and relatively sulfate-independent. Underlying mechanisms likely include overexpression of SULTR1;2 and SULTR2;1, which may additionally have evolved enhanced specificity for selenate over sulfate.

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.

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.

Impairing both HMA4 homeologs is required for cadmium reduction in tobacco

In tobacco, the heavy metal P1B-ATPases HMA4.1 and HMA4.2 function in root-to-shoot zinc and cadmium transport. We present greenhouse and field data that dissect the possibilities to impact the two homeologous genes in order to define the best strategy for leaf cadmium reduction. In a first step, both genes were silenced using an RNAi approach leading to >90% reduction of leaf cadmium content. To modulate HMA4 function more precisely, mutant HMA4.1 and HMA4.2 alleles of a Targeting Induced Local Lesions IN Genomes (TILLING) population were combined. As observed with RNAi plants, knockout of both homeologs decreased cadmium root-to-shoot transfer by >90%. Analysis of plants with segregating null and wild-type alleles of both homeologs showed that one functional HMA4 allele is sufficient to maintain wild-type cadmium levels. Plant development was affected in HMA4 RNAi and double knockout plants that included retarded growth, necrotic lesions, altered leaf morphology and increased water content. The combination of complete functional loss (nonsense mutation) in one homeologous HMA4 gene and the functional reduction in the other HMA4 gene (missense mutation) is proposed as strategy to limit cadmium leaf accumulation without developmental effects.

Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe

Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among-population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was carried out using a combination of new chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographic coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the southern Massif Central prior to last glacial maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison with the species history, but certainly before the establishment of anthropogenic metalliferous sites. Our results suggest that the large-scale genetic structure of N. caerulescens populations pre-existed to the local adaptation to metalliferous sites. The population structure of quantitative variation for metal-related adaptive traits must have established independently in isolated gene pools. However, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal-related traits and subunits isolation. Finally, admixture signals among distant metallicolous populations suggest a putative role of human activities in facilitating long-distance genetic exchanges.

A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain

Rice is a major source of calories and mineral nutrients for over half the world's human population. However, little is known in rice about the genetic basis of variation in accumulation of copper (Cu), an essential but potentially toxic nutrient. Here we identify OsHMA4 as the likely causal gene of a quantitative trait locus controlling Cu accumulation in rice grain. We provide evidence that OsHMA4 functions to sequester Cu into root vacuoles, limiting Cu accumulation in the grain. The difference in grain Cu accumulation is most likely attributed to a single amino acid substitution that leads to different OsHMA4 transport activity. The allele associated with low grain Cu was found in 67 of the 1,367 rice accessions investigated. Identification of natural allelic variation in OsHMA4 may facilitate the development of rice varieties with grain Cu concentrations tuned to both the concentration of Cu in the soil and dietary needs.

Copper (Cu) is an essential mineral nutrient but high concentrations in rice grain can cause toxicity. Here the authors provide evidence that natural variation in rice grain Cu concentration is caused by altered sequestration of Cu into root vacuoles due to a single amino acid substitution in the OsHMA4 transporter.

Expression of the ZNT1 Zinc Transporter from the Metal Hyperaccumulator Noccaea caerulescens Confers Enhanced Zinc and Cadmium Tolerance and Accumulation to Arabidopsis thaliana

Prompt regulation of transition metal transporters is crucial for plant zinc homeostasis. NcZNT1 is one of such transporters, found in the metal hyperaccumulator Brassicaceae species Noccaea caerulescens. It is orthologous to AtZIP4 from Arabidopsis thaliana, an important actor in Zn homeostasis. We examined if the NcZNT1 function contributes to the metal hyperaccumulation of N. caerulescens. NcZNT1 was found to be a plasma-membrane located metal transporter. Constitutive overexpression of NcZNT1 in A. thaliana conferred enhanced tolerance to exposure to excess Zn and Cd supply, as well as increased accumulation of Zn and Cd and induction of the Fe deficiency response, when compared to non-transformed wild-type plants. Promoters of both genes were induced by Zn deficiency in roots and shoots of A. thaliana. In A. thaliana, the AtZIP4 and NcZNT1 promoters were mainly active in cortex, endodermis and pericycle cells under Zn deficient conditions. In N. caerulescens, the promoters were active in the same tissues, though the activity of the NcZNT1 promoter was higher and not limited to Zn deficient conditions. Common cis elements were identified in both promoters by 5' deletion analysis. These correspond to the previously determined Zinc Deficiency Responsive Elements found in A. thaliana to interact with two redundantly acting transcription factors, bZIP19 and bZIP23, controlling the Zn deficiency response. In conclusion, these results suggest that NcZNT1 is an important factor in contributing to Zn and Cd hyperaccumulation in N. caerulescens. Differences in cis- and trans-regulators are likely to account for the differences in expression between A. thaliana and N. caerulescens. The high, constitutive NcZNT1 expression in the stele of N. caerulescens roots implicates its involvement in long distance root-to-shoot metal transport by maintaining a Zn/Cd influx into cells responsible for xylem loading.

Metal binding to the N-terminal cytoplasmic domain of the PIB ATPase HMA4 is required for metal transport in Arabidopsis

PIB ATPases are metal cation pumps that transport metals across membranes. These proteins possess N- and C-terminal cytoplasmic extensions that contain Cys- and His-rich high affinity metal binding domains, which may be involved in metal sensing, metal ion selectivity and/or in regulation of the pump activity. The PIB ATPase HMA4 (Heavy Metal ATPase 4) plays a central role in metal homeostasis in Arabidopsis thaliana and has a key function in zinc and cadmium hypertolerance and hyperaccumulation in the extremophile plant species Arabidopsis halleri. Here, we examined the function and structure of the N-terminal cytoplasmic metal-binding domain of HMA4. We mutagenized a conserved CCTSE metal-binding motif in the domain and assessed the impact of the mutations on protein function and localization in planta, on metal-binding properties in vitro and on protein structure by Nuclear Magnetic Resonance spectroscopy. The two Cys residues of the motif are essential for the function, but not for localization, of HMA4 in planta, whereas the Glu residue is important but not essential. These residues also determine zinc coordination and affinity. Zinc binding to the N-terminal domain is thus crucial for HMA4 protein function, whereas it is not required to maintain the protein structure. Altogether, combining in vivo and in vitro approaches in our study provides insights towards the molecular understanding of metal transport and specificity of metal P-type ATPases.

Enhanced expression of SaHMA3 plays critical roles in Cd hyperaccumulation and hypertolerance in Cd hyperaccumulator Sedum alfredii Hance

The enhanced expression of a P 1B -type ATPase gene ( SaHMA3 ) is essential for Cd hyperaccumulation and hypertolerance in Sedum alfredii Hance. A functional understanding of the mechanism through which hyperaccumulator plants accumulate and tolerate extremely toxic metals is a prerequisite for the development of novel strategies for improving phytoremediation using engineered plants or natural hyperaccumulators as well as biofortification and food crop safety. Most hyperaccumulator species, however, are small and slow-growing, and their potential for large-scale decontamination of polluted soils is limited. Sedum alfredii Hance, the only one metal hyperaccumulator from the Crassulaceae family, is an ideal candidate for gaining a functional understanding of the intra-family hyperaccumulation mechanisms as well as their potential applications. In the present study, we isolated and functionally characterized a P1B-type ATPase gene (SaHMA3) from S. alfredii Hance. SaHMA3 alleles from a hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) were constitutively expressed in both shoot and root and encoded tonoplast-localized proteins, but showed differences in transport substrate specificity and expression level. SaHMA3 h from the HE plant was a Cd transporter. In contrast, SaHMA3n from NHE plants was able to transport both Zn and Cd. SaHMA3 showed a significantly higher constitutive expression level in HE plants than in NHE plants. Furthermore, the expression level of SaHMA3 in the shoots of HE plants was considerably higher than in the roots. Overexpression of SaHMA3h in tobacco plants significantly enhanced Cd tolerance and accumulation and greatly increased the root sequestration of Cd. In summary, our data suggested that SaHMA3 plays critical roles in Cd hyperaccumulation and hypertolerance in Cd hyperaccumulator S. alfredii Hance.

Characterization of Zinc and Cadmium Hyperaccumulation in Three Noccaea (Brassicaceae) Populations from Non-metalliferous Sites in the Eastern Pyrenees

The Southern slope of the Pyrenees is the meridional limit for the distribution of several Noccaea populations. However, the systematic description of these populations and their hyperaccumulation mechanisms are not well established. Morphological and genetic analysis (ITS and 3 chloroplast regions) were used to identify Noccaea populations localized on non-metallicolous soils during a survey in the Catalonian Pyrenees. Cd and Zn concentrations were analyzed in soils and plants both sampled in the field and grown hydroponically. The expression of selected metal transporter genes was assessed by quantitative PCR. The populations were identified as Noccaea brachypetala (Jord.) F.K. Mey by conspicuous morphological traits. Principal component analysis provided a clear separation among N. brachypetala, Noccaea caerulescens J. Presl & C. Presl and Noccaea occitanica (Jord.) F.K. Mey., three Noccaea species reported in the Pyrenees. Contrastingly, ITS and cpDNA analyses were unable to clearly differentiate these taxa. Differences in the expression of the metal transporter genes HMA3, HMA4, and MTP1 between N. caerulescens and N. brachypetala, and those amongst the N. brachypetala populations suggest differences in the strategies for handling enhanced Cd and Zn availability. This is the first report demonstrating Cd and Zn hyperaccumulation by N. brachypetala both in the field and in hydroponics. This comprehensive study based on taxonomic, molecular, and physiological data allows both the correct identification of this species and the characterization of population differences in hyperaccumulation and tolerance of Zn and Cd.

Functional analysis of the three HMA4 copies of the metal hyperaccumulator Arabidopsis halleri

In Arabidopsis halleri, the HMA4 gene has an essential function in Zn/Cd hypertolerance and hyperaccumulation by mediating root-to-shoot translocation of metals. Constitutive high expression of AhHMA4 results from a tandem triplication and cis-activation of the promoter of all three copies. The three AhHMA4 copies possess divergent promoter sequences, but highly conserved coding sequences, and display identical expression profiles in the root and shoot vascular system. Here, an AhHMA4::GFP fusion was expressed under the control of each of the three A. halleri HMA4 promoters in a hma2hma4 double mutant of A. thaliana to individually examine the function of each AhHMA4 copy. The protein showed non-polar localization at the plasma membrane of the root pericycle cells of both A. thaliana and A. halleri. The expression of each AhHMA4::GFP copy complemented the severe Zn-deficiency phenotype of the hma2hma4 mutant by restoring root-to-shoot translocation of Zn. However, each copy had a different impact on metal homeostasis in the A. thaliana genetic background: AhHMA4 copies 2 and 3 were more highly expressed and provided higher Zn tolerance in roots and accumulation in shoots than copy 1, and AhHMA4 copy 3 also increased Cd tolerance in roots. These data suggest a certain extent of functional differentiation among the three A. halleri HMA4 copies, stemming from differences in expression levels rather than in expression profile. HMA4 is a key node of the Zn homeostasis network and small changes in expression level can have a major impact on Zn allocation to root or shoot tissues.

Got to hide your Zn away: Molecular control of Zn accumulation and biotechnological applications

Zinc (Zn) is an essential micronutrient for all organisms, with key catalytic and structural functions. Zn deficiency in plants, common in alkaline soils, results in growth arrest and sterility. On the other hand, Zn can become toxic at elevated concentrations. Several studies revealed molecules involved with metal acquisition in roots, distribution within the plant and translocation to seeds. Transmembrane Zn transport proteins and Zn chelators are involved in avoiding its toxic effects. Plant species with the capacity to hyperaccumulate and hypertolerate Zn have been characterized. Plants that accumulate and tolerate high amounts of Zn and produce abundant biomass may be useful for phytoremediation, allowing cleaning of metal-contaminated soils. The study of Zn hyperaccumulators may provide indications of genes and processes useful for biofortification, for developing crops with high amounts of nutrients in edible tissues. Future research needs to focus on functional characterization of Zn transporters in planta, elucidation of Zn uptake and sensing mechanisms, and on understanding the cross-talk between Zn homeostasis and other physiological processes. For this, new research should use multidisciplinary approaches, combining traditional and emerging techniques, such as genome-encoded metal sensors and multi-element imaging, quantification and speciation using synchrotron-based methods.

Intraspecific variability of cadmium tolerance and accumulation, and cadmium-induced cell wall modifications in the metal hyperaccumulator Arabidopsis halleri

Certain molecular mechanisms of Cd tolerance and accumulation have been identified in the model species Arabidopsis halleri, while intraspecific variability of these traits and the mechanisms of shoot detoxification were little addressed. The Cd tolerance and accumulation of metallicolous and non-metallicolous A. halleri populations from different genetic units were tested in controlled conditions. In addition, changes in shoot cell wall composition were investigated using Fourier transform infrared spectroscopy. Indeed, recent works on A. halleri suggest Cd sequestration both inside cells and in the cell wall/apoplast. All A. halleri populations tested were hypertolerant to Cd, and the metallicolous populations were on average the most tolerant. Accumulation was highly variable between and within populations, and populations that were non-accumulators of Cd were identified. The effect of Cd on the cell wall composition was quite similar in the sensitive species A. lyrata and in A. halleri individuals; the pectin/polysaccharide content of cell walls seems to increase after Cd treatment. Nevertheless, the changes induced by Cd were more pronounced in the less tolerant individuals, leading to a correlation between the level of tolerance and the extent of modifications. This work demonstrated that Cd tolerance and accumulation are highly variable traits in A. halleri, suggesting adaptation at the local scale and involvement of various molecular mechanisms. While in non-metallicolous populations drastic modifications of the cell wall occur due to higher Cd toxicity and/or Cd immobilization in this compartment, the increased tolerance of metallicolous populations probably involves other mechanisms such as vacuolar sequestration.

Evidence of various mechanisms of Cd sequestration in the hyperaccumulator Arabidopsis halleri, the non-accumulator Arabidopsis lyrata, and their progenies by combined synchrotron-based techniques

Arabidopsis halleri is a model plant for Zn and Cd hyperaccumulation. The objective of this study was to determine the relationship between the chemical forms of Cd, its distribution in leaves, and Cd accumulation and tolerance. An interspecific cross was carried out between A. halleri and the non-tolerant and non-hyperaccumulating relative A. lyrata providing progenies segregating for Cd tolerance and accumulation. Cd speciation and distribution were investigated using X-ray absorption spectroscopy and microfocused X-ray fluorescence. In A. lyrata and non-tolerant progenies, Cd was coordinated by S atoms only or with a small contribution of O groups. Interestingly, the proportion of O ligands increased in A. halleri and tolerant progenies, and they were predominant in most of them, while S ligands were still present. Therefore, the binding of Cd with O ligands was associated with Cd tolerance. In A. halleri, Cd was mainly located in the xylem, phloem, and mesophyll tissue, suggesting a reallocation process for Cd within the plant. The distribution of the metal at the cell level was further discussed. In A. lyrata, the vascular bundles were also Cd enriched, but the epidermis was richer in Cd as compared with the mesophyll. Cd was identified in trichomes of both species. This work demonstrated that both Cd speciation and localization were related to the tolerance character of the plant.

Molecular and biochemical properties of two P1B2-ATPases, CsHMA3 and CsHMA4, from cucumber

P1B-ATPases (heavy metal ATPases, HMAs) constitute a multigenic subfamily of P-ATPases involved in the transport of monovalent and divalent heavy metals in plant cells. Here, we present the organization of genes encoding the HMA family in the cucumber genome and report the function and biochemical properties of two cucumber proteins homologous to the HMA2-4-like plant HMAs. Eight genes encoding putative P1B -ATPases were identified in the cucumber genome. Among them, CsHMA3 was predominantly expressed in roots and up-regulated by Pb, Zn and Cd excess, whereas the CsHMA4 transcript was most abundant in roots and flowers of cucumber plants, and elevated under Pb and Zn excess. Expression of CsHMA3 in Saccharomyces cerevisiae enhanced yeast tolerance to Cd and Pb, whereas CsHMA4 conferred increased resistance of yeast cells to Cd and Zn. Immunostaining with specific antibodies raised against cucumber proteins revealed tonoplast localization of CsHMA3 and plasma membrane localization of CsHMA4 in cucumber root cells. Kinetic studies of CsHMA3 and CsHMA4 in yeast membranes indicated differing heavy metal cation affinities of these two proteins. Altogether, the results suggest an important role of CsHMA3 and CsHMA4 in Cd and Pb detoxification and Zn homeostasis in cucumber cells.

Genotypic variations in the dynamics of metal concentrations in poplar leaves: a field study with a perspective on phytoremediation

Poplar is commonly used for phytoremediation of metal polluted soils. However, the high concentrations of trace elements present in leaves may return to soil upon leaf abscission. To investigate the mechanisms controlling leaf metal content, metal concentrations and expression levels of genes involved in metal transport were monitored at different developmental stages on leaves from different poplar genotypes growing on a contaminated field. Large differences in leaf metal concentrations were observed among genotypes. Whereas Mg was remobilized during senescence, Zn and Cd accumulation continued until leaf abscission in all genotypes. A positive correlation between Natural Resistance Associated Macrophage Protein 1 (NRAMP1) expression levels and Zn bio-concentration factors was observed. Principal component analyses of metal concentrations and gene expression levels clearly discriminated poplar genotypes. This study highlights a general absence of trace element remobilization from poplar leaves despite genotype specificities in the control of leaf metal homeostasis.

RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc

Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession "Ganges" by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.

Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics.

The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation

Nickel is an economically important metal and phytotechnologies are being developed to limit the impact of nickel mining on the environment. More than 300 plant species are known to hyperaccumulate nickel. However, our knowledge of the mechanisms involved in nickel accumulation in plants is very limited because it has not yet been possible to study these hyperaccumulators at the genomic level. Here, we used next-generation sequencing technologies to sequence the transcriptome of the nickel hyperaccumulator Psychotria gabriellae of the Rubiaceae family, and used yeast and Arabidopsis as heterologous systems to study the activity of identified metal transporters. We characterized the activity of three metal transporters from the NRAMP and IREG/FPN families. In particular, we showed that PgIREG1 is able to confer nickel tolerance when expressed in yeast and in transgenic plants, where it localizes in the tonoplast. In addition, PgIREG1 shows higher expression in P. gabriellae than in the related non-accumulator species Psychotria semperflorens. Our results designate PgIREG1 as a candidate gene for nickel tolerance and hyperaccumulation in P. gabriellae. These results also show how next-generation sequencing technologies can be used to access the transcriptome of non-model nickel hyperaccumulators to identify the underlying molecular mechanisms.

Zinc export results in adaptive zinc tolerance in the ectomycorrhizal basidiomycete Suillus bovinus

On Zn-polluted soils, populations of the ectomycorrhizal basidiomycete Suillus bovinus exhibit an elevated Zn tolerance when compared to populations on non-polluted sites. To elucidate the mechanism of Zn tolerance, the time-course of Zn uptake was studied in isolates with contrasting Zn tolerance. Unidirectional fluxes and subcellular compartmentation of Zn were investigated through radiotracer flux analyses. Fluorescence imaging was used to support the subcellular Zn compartmentation. After 2 h of exposure to 200 μM Zn, significantly more Zn was accumulated in Zn-sensitive isolates compared to tolerant isolates, despite similar short-term uptake kinetics and similar extracellular Zn sequestration in cell walls. In Zn-sensitive isolates twice as much Zn accumulated in the cytoplasm and 12 times more Zn in the vacuole. (65)Zn efflux analyses revealed a considerably faster Zn export in the Zn-tolerant isolate. The adaptive Zn tolerance in S. bovinus is therefore achieved by a preferential removal of Zn out of the cytoplasm, back into the apoplast, instead of the usual transfer of Zn into the vacuole. Zn exclusion in the fungal symbiont eventually contributes to a lower Zn influx in host plants.