Elevated Expression of Vacuolar Nickel Transporter Gene IREG2 Is Associated With Reduced Root-to-Shoot Nickel Translocation in Noccaea japonica

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

Metal Interactions in the Ni Hyperaccumulating Population of Noccaea caerulescens Monte Prinzera

Hyperaccumulation is a fascinating trait displayed by a few plant species able to accumulate large amounts of metal ions in above-ground tissues without symptoms of toxicity. Noccaea caerulescens is a recognized model system to study metal hyperaccumulation and hypertolerance. A N. caerulescens population naturally growing on a serpentine soil in the Italian Apennine Mountains, Monte Prinzera, was chosen for the study here reported. Plants were grown hydroponically and treated with different metals, in excess or limiting concentrations. Accumulated metals were quantified in shoots and roots by means of ICP-MS. By real-time PCR analysis, the expression of metal transporters and Fe deficiency-regulated genes was compared in the shoots and roots of treated plants. N. caerulescens Monte Prinzera confirmed its ability to hypertolerate and hyperaccumulate Ni but not Zn. Moreover, excess Ni does not induce Fe deficiency as in Ni-sensitive species and instead competes with Fe translocation rather than its uptake.

Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana)

Understanding the genetic response of plants to nickel stress is a necessary step to improving the utility of plants in environmental remediation and restoration. The main objective of this study was to generate whole genome expression profiles of P. banksiana exposed to nickel ion toxicity compared to reference genotypes. Pinus banksiana seedlings were screened in a growth chamber setting using a high concentration of 1600 mg of nickel per 1 kg of soil. RNA was extracted and sequenced using the Illumina platform, followed by de novo transcriptome assembly. Overall, 25,552 transcripts were assigned gene ontology. The biological processes in water-treated samples were analyzed, and 55% of transcripts were distributed among five categories: DNA metabolic process (19.3%), response to stress (13.3%), response to chemical stimuli (8.7%), signal transduction (7.7%) and response to biotic stimulus (6.0%). For molecular function, the highest percentages of genes were involved in nucleotide binding (27.6%), nuclease activity (27.3%) and kinase activity (10.3%). Sixty-two percent of genes were associated with cellular compartments. Of these genes, 21.7% were found in the plasma membrane, 16.1% in the cytosol, 12.4% with the chloroplast and 11.9% in the extracellular region. Nickel ions induced changes in gene expression, resulting in the emergence of differentially regulated categories. Overall, there were significant changes in gene expression with a total 4128 genes upregulated and 3754 downregulated genes detected in nickel-treated genotypes compared to water-treated control plants. For biological processes, the highest percentage of upregulated genes in plants exposed to nickel were associated with the response to stress (15%), the response to chemicals (11,1%), carbohydrate metabolic processes (7.4%) and catabolic processes (7.4%). The largest proportions of downregulated genes were associated with the biosynthetic process (21%), carbohydrate metabolic process (14.3%), response to biotic stimulus (10.7%) and response to stress (10.7%). For molecular function, genes encoding for enzyme regulatory and hydrolase activities represented the highest proportion (61%) of upregulated gene. The majority of downregulated genes were involved in the biosynthetic processes. Overall, 58% of upregulated genes were located in the extracellular region and the nucleus, while 42% of downregulated genes were localized to the plasma membrane and 33% to the extracellular region. This study represents the first report of a transcriptome from a conifer species treated with nickel.

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.

Metal Tolerance Protein Encoding Gene Family in Fagopyrum tartaricum: Genome-Wide Identification, Characterization and Expression under Multiple Metal Stresses

Metal tolerance proteins (MTP) as divalent cation transporters are essential for plant metal tolerance and homeostasis. However, the characterization and the definitive phylogeny of the MTP gene family in Fagopyrum tartaricum, and their roles in response to metal stress are still unknown. In the present study, MTP genes in Fagopyrum tartaricum were identified, and their phylogenetic relationships, structural characteristics, physicochemical parameters, as well as expression profiles under five metal stresses including Fe, Mn, Cu, Zn, and Cd were also investigated. Phylogenetic relationship analysis showed that 12 Fagopyrum tartaricum MTP genes were classified into three major clusters and seven groups. All FtMTPs had typical structural features of the MTP gene family and were predicted to be located in the cell vacuole. The upstream region of FtMTPs contained abundant cis-acting elements, implying their functions in development progress and stress response. Tissue-specific expression analysis results indicated the regulation of FtMTPs in the growth and development of Fagopyrum tataricum. Besides, the expression of most FtMTP genes could be induced by multiple metals and showed different expression patterns under at least two metal stresses. These findings provide useful information for the research of the metal tolerance mechanism and genetic improvement of Fagopyrum tataricum.

Overexpression of ZNT1 and NRAMP4 from the Ni Hyperaccumulator Noccaea caerulescens Population Monte Prinzera in Arabidopsis thaliana Perturbs Fe, Mn, and Ni Accumulation

Metalliferous soils are characterized by a high content of metal compounds that can hamper plant growth. The pseudometallophyte Noccaea caerulescens is able to grow on metalliferous substrates by implementing both tolerance and accumulation of usually toxic metal ions. Expression of particular transmembrane transporter proteins (e.g., members of the ZIP and NRAMP families) leads to metal tolerance and accumulation, and its comparison between hyperaccumulator N. caerulescens with non-accumulator relatives Arabidopsis thaliana and Thlaspi arvense has deepened our knowledge on mechanisms adopted by plants to survive in metalliferous soils. In this work, two transporters, ZNT1 and NRAMP4, expressed in a serpentinic population of N. caerulescens identified on the Monte Prinzera (Italy) are considered, and their expression has been induced in yeast and in A. thaliana. In the latter, single transgenic lines were crossed to test the effect of the combined over-expression of the two transporters. An enhanced iron and manganese translocation towards the shoot was induced by overexpression of NcZNT1. The combined overexpression of NcZNT1 and NcNRAMP4 did perturb the metal accumulation in plants.

Differences in mineral accumulation and gene expression profiles between two metal hyperaccumulators, Noccaea japonica and Noccaea caerulescens ecotype Ganges, under excess nickel condition

Here we compare mineral accumulation and global gene expression patterns between two metal hyperaccumulator plants - Noccaea japonica, originating from Ni-rich serpentine soils, and Noccaea caerulescens (ecotype Ganges), originating from Zn/Pb-mine soils - under excess Ni conditions. Significant differences in the accumulation of K, P, Mg, B, and Mo were explained by the expression levels of specific transporters for each mineral. We previously showed that total Ni accumulation in the whole plant is higher in N. caerulescens than in N. japonica. Here we found a similar tendency for Fe under excess Ni; however, the expression of iron-regulated transporter 1 (IRT1), which encodes the primary Fe uptake transporter and causes excess Ni uptake in Arabidopsis thaliana, was higher in N. japonica. NjIRT1 has a point mutation at Asp100, which is essential for Fe transport, and so might lack its Fe and possibly Ni transport function. Noccaea japonica might have lost its IRT1 function, which would prevent excess Ni uptake via IRT1 in Ni-rich soils, and come to rely on other transporters.

Metal transporters in organelles and their roles in heavy metal transportation and sequestration mechanisms in plants

Heavy metal toxicity is one of the major concerns for agriculture and health. Accumulation of toxic heavy metals at high concentrations in edible parts of crop plants is the primary cause of disease in humans and cattle. A dramatic increase in industrialization, urbanization, and other high anthropogenic activities has led to the accumulation of heavy metals in agricultural soil, which has consequently disrupted soil conditions and affected crop yield. By now, plants have developed several mechanisms to cope with heavy metal stress. However, not all plants are equally effective in dealing with the toxicity of high heavy metal concentrations. Plants have modified their anatomy, morphophysiology, and molecular networks to survive under changing environmental conditions. Heavy metal sequestration is one of the essential processes evolved by some plants to deal with heavy metals' toxic concentration. Some plants even have the ability to accumulate metals in high quantities in the shoots/organelles without toxic effects. For intercellular and interorganeller metal transport, plants harbor spatially distributed various transporters which mainly help in uptake, translocation, and redistribution of metals. This review discusses different heavy metal transporters in different organelles and their roles in metal sequestration and redistribution to help plants cope with heavy metal stress. A good understanding of the processes at stake helps in developing more tolerant crops without affecting their productivity.

Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils

Noccaea brachypetala is a close relative of Noccaea caerulescens, a model plant species used in metal hyperaccumulation studies. In a previous survey in the Catalan Pyrenees, we found two occidental and two oriental N. brachypetala populations growing on non-metalliferous soils, with accumulated high concentrations of Cd and Zn. Our hypothesis was that the microbiome companion of the plant roots may influence the ability of these plants to absorb metals. We performed high-throughput sequencing of the bacterial and fungal communities in the rhizosphere soil and rhizoplane fractions. The rhizobiomes and shoot ionomes of N. brachypetala plants were analyzed along with those from other non-hyperaccumulator Brassicaceae species found at the same sampling locations. The analyses revealed that microbiome richness and relative abundance tended to increase in N. brachypetala plants compared to non-hyperaccumulator species, regardless of plant location. We confirmed that the root compartment is a key factor in describing the community composition linked to the cohabiting Brassicaceae species, and the rhizoplane fraction contained the specific and rare taxa associated with each species. N. brachypetala plants harbored a similar relative abundance of fungi compared to the other plant hosts, but there was a notable reduction in some specific taxa. Additionally, we observed an enrichment in the hyperaccumulator rhizoplane of previously described metal-tolerant bacteria and bacteria involved in nitrogen cycling. The bacteria involved in the nitrogen cycle could contribute indirectly to the hyperaccumulator phenotype by improving soil quality and fertility. Our results indicate that N. brachypetala captures a particular prokaryotic community from the soil. This particular prokaryotic community may benefit the extraction of metal ions and/or improve plant nutrition. Our research identified satellite groups associated with the root niche of a hyperaccumulator plant that may assist in improving biological strategies in heavy metal remediation.

Root hairs: the villi of plants

Strikingly, evolution shaped similar tubular structures at the µm to mm scale in roots of sessile plants and in small intestines of mobile mammals to ensure an efficient transfer of essential nutrients from 'dead matter' into biota. These structures, named root hairs (RHs) in plants and villi in mammals, numerously stretch into the environment, and extremely enlarge root and intestine surfaces. They are believed to forage for nutrients, and mediate their uptake. While the conceptional understanding of plant RH function in hydromineral nutrition seems clear, experimental evidence presented in textbooks is restricted to a very limited number of reference-nutrients. Here, we make an element-by-element journey through the periodic table and link individual nutrient availabilities to the development, structure/shape and function of RHs. Based on recent developments in molecular biology and the identification of mutants differing in number, length or other shape-related characteristics of RHs in various plant species, we present comprehensive advances in (i) the physiological role of RHs for the uptake of specific nutrients, (ii) the developmental and morphological responses of RHs to element availability and (iii) RH-localized nutrient transport proteins. Our update identifies crucial roles of RHs for hydromineral nutrition, mostly under nutrient and/or water limiting conditions, and highlights the influence of certain mineral availabilities on early stages of RH development, suggesting that nutritional stimuli, as deficiencies in P, Mn or B, can even dominate over intrinsic developmental programs underlying RH differentiation.

Wide cross-species RNA-Seq comparison reveals convergent molecular mechanisms involved in nickel hyperaccumulation across dicotyledons

The Anthropocene epoch is associated with the spreading of metals in the environment increasing oxidative and genotoxic stress on organisms. Interestingly, c. 520 plant species growing on metalliferous soils acquired the capacity to accumulate and tolerate a tremendous amount of nickel in their shoots. The wide phylogenetic distribution of these species suggests that nickel hyperaccumulation evolved multiple times independently. However, the exact nature of these mechanisms and whether they have been recruited convergently in distant species is not known. To address these questions, we have developed a cross-species RNA-Seq approach combining differential gene expression analysis and cluster of orthologous group annotation to identify genes linked to nickel hyperaccumulation in distant plant families. Our analysis reveals candidate orthologous genes encoding convergent function involved in nickel hyperaccumulation, including the biosynthesis of specialized metabolites and cell wall organization. Our data also point out that the high expression of IREG/Ferroportin transporters recurrently emerged as a mechanism involved in nickel hyperaccumulation in plants. We further provide genetic evidence in the hyperaccumulator Noccaea caerulescens for the role of the NcIREG2 transporter in nickel sequestration in vacuoles. Our results provide molecular tools to better understand the mechanisms of nickel hyperaccumulation and study their evolution in plants.