Transcriptomic analysis of cadmium stress response in the heavy metal hyperaccumulator Sedum alfredii Hance

Lead-induced changes in plant cell ultrastructure: an overview

Lead (Pb) is one of the most harmful toxic metals and causes severe damage to plants even at low concentrations. Pb inhibits plant development, reduces photosynthesis rates, and causes metabolic disfunctions. Plant cells display these alterations in the form of abnormal morphological modifications resulting from ultrastructural changes in the cell wall, plasma membrane, chloroplast, endoplasmic reticulum, mitochondria, and nuclei. Depending on plant tolerance capacity, the ultrastructural changes could be either a sign of toxicity that limits plant development or an adaptive strategy to cope with Pb stress. This paper gathers data on Pb-induced changes in cell ultrastructure observed in many tolerant and hyperaccumulator plants and describes the ultrastructural changes that appear to be mechanisms to alleviate Pb toxicity. The different modifications caused by Pb in cell organelles are summarized and reinforced with hypotheses that provide an overview of plant responses to Pb stress and explain the physiological and morphological changes that occur in tolerant plants. These ultrastructural modifications could help assess the potential of plants for use in phytoremediation.

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.

Comparative transcriptome analysis between two different cadmium-accumulating genotypes of soybean (Glycine max) in response to cadmium stress

BACKGROUND

Cadmium (Cd) is extremely toxic and non-essential for plants. Different soybean varieties differ greatly in their Cd accumulation ability, but little is known about the underlying molecular mechanisms.

RESULTS

Here, we performed transcriptomic analysis using Illumina pair-end sequencing on root tissues from two soybean varieties (su8, high-Cd-accumulating (HAS) and su7, low Cd-accumulating (LAS)) grown with 0 or 50 μM CdSO4. A total of 18.76 million clean reads from the soybean root samples were obtained after quality assessment and data filtering. After Cd treatment, 739 differentially expressed genes (DEGs; 265 up and 474 down) were found in HAS; however, only 259 DEGs (88 up and 171 down) were found in LAS, and 64 genes were same between the two varieties. Pathway enrichment analysis suggested that after cadmium treatment, the DEGs between LAS and HAS were mainly enriched in glutathione metabolism and plant-pathogen interaction pathways. KEGG analysis showed that phenylalanine metabolism responding to cadmium stress in LAS, while ABC transporters responding to cadmium stress in HAS. Besides we found more differential expressed heavy metal transporters such as ABC transporters and zinc transporters in HAS than LAS, and there were more transcription factors differently expressed in HAS than LAS after cadmium treatment in two soybean varieties, eg. bHLH transcription factor, WRKY transcription factor and ZIP transcription factor.

CONCLUSIONS

Findings from this study will shed new insights on the underlying molecular mechanisms behind the Cd accumulation in soybean.

Identification and expression analysis of expansin gene family in Salvia miltiorrhiza

BACKGROUND

Expansins (EXP) are important enzymes that are involved in the extension of plant cells and regulation of root configurations, which play important roles in resisting various stresses. As a model medicinal plant, Salvia miltiorrhiza is well recognized for treating coronary heart disease, myocardial infection, and other cardiovascular and cerebrovascular diseases; however, the SmEXP gene family has not yet been analyzed.

METHODS

The SmEXP family was systematically analyzed using bioinformatics. Quantitative real-time PCR was employed to analyze the tissue expression patterns of the SmEXP family, as well as its expression under abscisic acid (ABA) treatment and abiotic stress. Subcellular localization assay revealed the localization of SmEXLA1, SmEXLB1, and SmEXPA2.

RESULTS

This study identified 29 SmEXP that belonged to four different subfamilies. SmEXP promoter analysis suggested that it may be involved in the growth, development, and stress adaptation of S. miltiorrhiza. An analysis of the expression patterns of SmEXP revealed that ABA, Cu2+, and NaCl had regulatory effects on its expression. A subcellular localization assay showed that SmEXLA1 and SmEXLB1 were located on the nucleus and cell membrane, while SmEXPA2 was located on the cell wall.

CONCLUSION

For this study, the SmEXP family was systematically analyzed for the first time, which lays a foundation for further elucidating its physiological and biological functionality.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Comparative transcriptomic analysis provides key genetic resources in clove basil (Ocimum gratissimum) under cadmium stress

Planting aromatic plant might be a promising strategy for safely utilizing heavy metal (HM)-contaminated soils, as HMs in essential oil could be completely excluded using some special technologies with ease. Clove basil (Ocimum gratissimum L.) is an important aromatic plant used in essential oil production. Improving cadmium (Cd) tolerance in clove basil can increase its production and improve the utilization efficiency of Cd-contaminated soils. However, the lack of genomic information on clove basil greatly restricts molecular studies and applications in phytoremediation. In this study, we demonstrated that high levels of Cd treatments (0.8, 1.6 and 6.5 mg/L) significantly impacted the growth and physiological attributes of clove basil. Cd contents in clove basil tissues increased with treatment concentrations. To identify Cd stress-responsive genes, we conducted a comparative transcriptomic analysis using seedlings cultured in the Hoagland's solution without Cd ion (control) or containing 1.6 mg/L CdCl2 (a moderate concentration of Cd stress for clove basil seedlings). A total of 104.38 Gb clean data with high-quality were generated in clove basil under Cd stress through Illumina sequencing. More than 1,800 differential expressed genes (DEGs) were identified after Cd treatment. The reliability and reproducibility of the transcriptomic data were validated through qRT-PCR analysis and Sanger sequencing. KEGG classification analysis identified the "MAPK signaling pathway," "plant hormone signal transduction" and "plant-pathogen interaction" as the top three pathways. DEGs were divided into five clusters based on their expression patterns during Cd stress. The functional annotation of DEGs indicated that downregulated DEGs were mainly involved in the "photosynthesis system," whereas upregulated DEGs were significantly assigned to the "MAPK signaling pathway" and "plant-pathogen interaction pathway." Furthermore, we identified a total of 78 transcription factors (TFs), including members of bHLH, WRKY, AP2/ERF, and MYB family. The expression of six bHLH genes, one WRKY and one ERF genes were significantly induced by Cd stress, suggesting that these TFs might play essential roles in regulating Cd stress responses. Overall, our study provides key genetic resources and new insights into Cd adaption mechanisms in clove basil.

Metabolome and transcriptome association analysis revealed key factors involved in melatonin mediated cadmium-stress tolerance in cotton

Cadmium (Cd), a non-essential element for plant, is a ubiquitous and highly toxic heavy metal, seriously endangering agricultural production and human health. As a nonedible economic crop, cotton (Gossypium hirsutum L.) has great potential in remediation of Cd contaminated soil, but its underlying mechanism is still unknown. Melatonin (MT), as a plant growth regulator, is involved in alleviating Cd toxicity in some plants, but the molecular mechanisms of MT-mediated Cd detoxification in cotton are largely unknown. This study investigated the possible molecular mechanisms of the MT-mediated Cd detoxification in cotton seedlings by comparative transcriptomic and metabolomic analyses. The results showed that the cotton seedlings were dwarfed and the leaves were wilted and yellow under Cd stress. The application of 50 µmol L^-1 MT significantly increased the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content under Cd stress, but 100 µmol L^-1 MT significantly decreased SOD activity, while increased ascorbate peroxidase (APX) activity significantly. The addition of 100 μmol L^-1 MT significantly increased Cd concentration in the shoots and roots under Cd stress. RNA-seq analysis showed that 5573, 7105, 7253, 25, 198, 9 up-regulated and 6644, 7192, 7404, 9, 59, 0 down-regulated differentially expressed genes (DEGs) were identified in the comparisons of CK vs T1, CK vs T2, CK vs T3, T1 vs T2, T1 vs T3 and T2 vs T3, respectively. It was revealed that MT promoted the expression of certain related genes under Cd stress, and the effect of 100 µmol L^-1 MT was better. Moreover, UPLC-MS/MS widely targeted metabolites analyses showed that 195, 150, 150, 12, 24, 59 up-regulated and 16, 11, 23, 38, 127, 66 down-regulated differentially accumulated metabolites (DAMs) were changed in the CK vs T1, CK vs T2, CK vs T3, T1 vs T2, T1 vs T3 and T2 vs T3, respectively. It was revealed that MT induced the synthesis of alkaloids and flavonoids, and inhibited or reduced the synthesis of lipids, amino acids and their derivatives. The comprehensive analyses of transcriptomic and metabolic data showed that 33 DEGs and 4 DAMs, 46 DEGs and 16 DAMs, and 1 DEGs and 1 DAMs were dominantly involved in the pathways of valine, leucine and isoleucine degradation, ABC transporter, alpha-linolenic acid metabolism, respectively. It was revealed that there were three major mechanisms involved in MT-mediated Cd detoxification in cotton, including the enhancement of antioxidant capacity regulated by APX, flavonoids and alkaloids; accumulation of secondary metabolites related to Cd chelation, such as amino acids and derivatives; and regulation of cadmium ion transportation, such as ABC transporter activation. In conclusion, this study provides new insights into the MT-mediated Cd stress response.

Proteomic Changes in Paspalum fasciculatum Leaves Exposed to Cd Stress

(1) Background: Cadmium is a toxic heavy metal that is widely distributed in water, soil, and air. It is present in agrochemicals, wastewater, battery waste, and volcanic eruptions. Thus, it can be absorbed by plants and enter the trophic chain. P. fasciculatum is a plant with phytoremediation capacity that can tolerate Cd stress, but changes in its proteome related to this tolerance have not yet been identified. (2) Methods: We conducted a quantitative analysis of the proteins present in P. fasciculatum leaves cultivated under greenhouse conditions in mining soils doped with 0 mg kg−1 (control), 30 mg kg−1, or 50 mg kg−1. This was carried out using the label-free shotgun proteomics technique. In this way, we determined the changes in the proteomes of the leaves of these plants, which allowed us to propose some tolerance mechanisms involved in the response to Cd stress. (3) Results: In total, 329 variable proteins were identified between treatments, which were classified into those associated with carbohydrate and energy metabolism; photosynthesis; structure, transport, and metabolism of proteins; antioxidant stress and defense; RNA and DNA processing; and signal transduction. (4) Conclusions: Based on changes in the differences in the leaf protein profiles between treatments, we hypothesize that some proteins associated with signal transduction (Ras-related protein RABA1e), HSPs (heat shock cognate 70 kDa protein 2), growth (actin-7), and cellular development (actin-1) are part of the tolerance response to Cd stress.

Comparative Analysis of Italian Lettuce (Lactuca sativa L. var. ramose) Transcriptome Profiles Reveals the Molecular Mechanism on Exogenous Melatonin Preventing Cadmium Toxicity

Cadmium (Cd) accumulation in lettuce causes a large amount of yield loss during industry. Although many studies report that exogenous melatonin helps to alleviate the Cd stress of lettuce, the molecular mechanism for how plant tissue responds to Cd treatment is unclear. Herein, we applied both PacBio and Illumina techniques for Italian lettuce under different designed treatments of Cd and melatonin, aiming to reveal the potential molecular pathway of the response to Cd stress as well as the how the pre-application of exogenous melatonin affect this process. This result reveals that the root has the biggest expression pattern shift and is a more essential tissue to respond to both Cd and melatonin treatments than leaves. We reveal the molecular background of the Cd stress response in prospects of antioxidant and hormone signal transduction pathways, and we found that their functions are diverged and specifically expressed in tissues. We also found that candidate genes related to melatonin detoxify during Cd stress. Our study sheds new light for future research on how melatonin improves the cadmium resistance of lettuce and also provide valuable data for lettuce breeding.

Transcriptomic Analysis of Cadmium Stressed Tamarix hispida Revealed Novel Transcripts and the Importance of Abscisic Acid Network

Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on the desert and soil with 0.5 to 1% salt content, making it an ideal plant for the research on response to abiotic stresses. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida. In the study, RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 μmol L^-1 CdCl₂ for 24, 48, and 72 h compared with control. In total, 72,764 unigenes exhibited similar sequences in the Non-redundant nucleic acid database (NR database), while 36.3% of all these unigenes may be new transcripts. In addition, 6,778, 8,282, and 8,601 DEGs were detected at 24, 48, and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance Cd resistance ability of T. hispida by regulating the production of ROS under Cd stress and inhibit absorption of Cd. The new transcriptome resources and data that we present in this study for T. hispida may facilitate investigation of molecular mechanisms governing Cd resistance.

A Novel NCSTN Mutation in a Three-Generation Chinese Family with Hidradenitis Suppurative

Objective

Hidradenitis suppurativa (HS) is a rare autosomal dominant condition characterized by inflamed nodules, cysts, deep abscesses, draining sinuses in the axillae, inguinal, and anogenital regions. Mutations in the NCSTN gene have been perceived to be responsible for the major underlying changes in the disorder. The purpose of this study is to identify a novel gene mutation in a Chinese family with HS.

Methods

A Chinese family with HS present was investigated. The proband had manifested with multiple draining sinuses on the posterior neck, chest, bilateral axillae, and perineal regions. DNA was isolated from the peripheral blood of the family members. The encoding exons with introns of the NCSTN gene were analyzed by polymerase chain reactions (PCR) and direct DNA sequencing. Sanger sequencing was performed to confirm the next-generation sequencing results and to analyze each mutation's familial segregation. Furthermore, the identified mutation was localized onto a 3D structure model using the DeepView Swiss-PdbViewer 4.1 software.

Results

In this family comprising 10 HS patients, one novel mutation of the NCSTN gene was identified, involving a deletion mutation (c.447delC(p.N150Ifs∗52)) in the NCSTN gene resulting in a frameshift and the new formation of a hydrogen bond.

Conclusion

Our study reports the identification of a novel mutation that causes familial HS and could expand the spectrum of mutations in the γ-secretase genes underlying HS.

Comparative Transcriptomics Analysis of Roots and Leaves under Cd Stress in Calotropis gigantea L

Calotropis gigantea is often found in mining areas with heavy metal pollution. However, little is known about the physiological and molecular response mechanism of C. gigantea to Cd stress. In the present study, Cd tolerance characteristic of C. gigantea and the potential mechanisms were explored. Seed germination test results showed that C. gigantea had a certain Cd tolerance capacity. Biochemical and transcriptomic analysis indicated that the roots and leaves of C. gigantea had different responses to early Cd stress. A total of 176 and 1618 DEGs were identified in the roots and leaves of C. gigantea treated with Cd compared to the control samples, respectively. Results indicated that oxidative stress was mainly initiated in the roots of C. gigantea, whereas the leaves activated several Cd detoxification processes to cope with Cd, including the upregulation of genes involved in Cd transport (i.e., absorption, efflux, or compartmentalization), cell wall remodeling, antioxidant system, and chelation. This study provides preliminary information to understand how C. gigantea respond to Cd stress, which is useful for evaluating the potential of C. gigantea in the remediation of Cd-contaminated soils.

Cadmium Exposure Alters Rhizospheric Microbial Community and Transcriptional Expression of Vetiver Grass

Vetiver grass (Chrysopogon zizanioides L.) has been used to remediate cadmium (Cd)-contaminated soil, while there have been few studies on the influence of Cd exposure on the rhizospheric microbial community and transcriptional expression of C. zizanioides. In this study, we investigated the response of the rhizospheric microbial community and transcriptional expression of C. zizanioides in 20 mg/kg Cd-contaminated soil. The results showed that Cd levels in the roots and shoots of C. zizanioides reached 250.80 and 73.40 mg/kg, respectively. The Cd exposure changed the rhizospheric bacterial community, resulting in the significant enrichment of Sphingomonas, Lysobacter, and Gemmatimonadetes in Cd-contaminated soil. In addition, 880 and 3,419 differentially expressed genes were identified in the plant roots and shoots, respectively, in response to Cd stress. Among these, the overexpressed genes associated with redox homeostasis, glutathione (GSH) metabolism, cell wall biosynthesis, and transmembrane transport pathways were found to participate in Cd detoxification in C. zizanioides. These findings could be useful for understanding the selective variation of the rhizospheric microbial community and the detoxification mechanisms of C. zizanioides in Cd phytoremediation.

Analysis of Cadmium-Stress-Induced microRNAs and Their Targets Reveals bra-miR172b-3p as a Potential Cd2+-Specific Resistance Factor in Brassica juncea

The contamination of soil with high levels of cadmium (Cd) is of increasing concern, as Cd is a heavy metal element that seriously limits crop productivity and quality, thus affecting human health. (1) Background: Some miRNAs play key regulatory roles in response to Cd stress, but few have been explored in the highly Cd-enriched coefficient oilseed crop, Brassica juncea. (2) Methods: The genome-wide identification and characterization of miRNAs and their targets in leaves and roots of Brassica juncea exposed to Cd stress was undertaken using strand specific transcript sequencing and miRNA sequencing. (3) Results: In total, 11 known and novel miRNAs, as well as 56 target transcripts, were identified as Cd-responsive miRNAs and transcripts. Additionally, four corresponding target transcripts of six miRNAs, including FLA9 (Fasciclin-Like Arabinogalactan-protein 9), ATCAT3 (catalase 3), DOX1 (dioxygenases) and ATCCS (copper chaperone for superoxide dismutase), were found to be involved in the plant’s biotic stress pathway. We further validated the expression of three miRNA and six target genes in response to Cd, hydrargyrum (Hg), manganese (Mn), plumbum (Pb) or natrium (Na) stress and Mucor infection by qRT-PCR, and show that ATCCS and FLA9 were significantly and differentially regulated in the Cd-treated leaves. In addition, our results showed that DOX1 was obviously induced by Pb stress. Among the respective target miRNAs, bra-miR172b-3p (target for ATCCS) and ra-miR398-3p (target for FLA9) were down-regulated in Cd-treated leaves. (4) Conclusions: We identified bra-miR172b-3p as a potential Cd-specific resistant inhibitor, which may be negatively regulated in ATCCS in response to Cd stress. These findings could provide further insight into the regulatory networks of Cd-responsive miRNA in Brassica juncea.

Comparative understanding of metal hyperaccumulation in plants: a mini-review

Hyperaccumulator plants are ideal models for investigating the regulatory mechanisms of plant metal homeostasis and environmental adaptation due to their notable traits of metal accumulation and tolerance. These traits may benefit either the biofortification of essential mineral nutrients or the phytoremediation of nonessential toxic metals. A common mechanism by which elevated expression of key genes involved in metal transport or chelation contributes to hyperaccumulation and hypertolerance was proposed mainly from studies examining two Brassicaceae hyperaccumulators, namely Arabidopsis halleri and Noccaea caerulescens (formerly Thlaspi caerulescens). Meanwhile, recent findings regarding systems outside the Brassicaceae hyperaccumulators indicated that functional enhancement of key genes might represent a strategy evolved by hyperaccumulator plants. This review provides a brief outline of metal hyperaccumulation in plants and highlights commonalities and differences among various hyperaccumulators.

Identification and characterization of SaeIF1 from the eukaryotic translation factor SUI1 family in cadmium hyperaccumulator Sedum alfredii

MAIN CONCLUSION

Cadmium-sensitive yeast screening resulted in the isolation of protein translation factor SaeIF1 from the hyperaccumulator Sedum alfredii which has both general and special regulatory roles in controlling cadmium accumulation. The hyperaccumulator of Sedum alfredii has the extraordinary ability to hyperaccumulate cadmium (Cd) in shoots. To investigate its underlying molecular mechanisms of Cd hyperaccumulation, a cDNA library was generated from leaf tissues of S. alfredii. SaeIF1, belonging to the eukaryotic protein translation factor SUI1 family, was identified by screening Cd-sensitive yeast transformants with this library. The full-length cDNA of SaeIF1 has 582 bp and encodes a predicted protein with 120 amino acids. Transient expression assays showed subcellular localization of SaeIF1 in the cytoplasm. SaeIF1 was constitutively and highly expressed in roots and shoots of the hyperaccumulator of S. alfredii, while its transcript levels showed over 100-fold higher expression in the hyperaccumulator of S. alfredii relative to the tissues of a nonhyperaccumulating ecotype of S. alfredii. However, the overexpression of SaeIF1 in yeast cells increased Cd accumulation, but conferred more Cd sensitivity. Transgenic Arabidopsis thaliana expressing SaeIF1 accumulated more Cd in roots and shoots without changes in the ratio of Cd content in shoots and roots, but were more sensitive to Cd stress than wild type. Both special and general roles of SaeIF1 in Cd uptake, transportation, and detoxification are discussed, and might be responsible for the hyperaccumulation characteristics of S. alfredii.

Molecular mechanisms of plant adaptive responses to heavy metals stress

Heavy metals (HMs) are among the main environmental pollutants that can enter the soil, water bodies, and the atmosphere as a result of natural processes (weathering of rocks, volcanic activity), and also as a result of human activities (mining, metallurgical and chemical industries, transport, application of mineral fertilizers). Plants counteract the HMs stresses through morphological and physiological adaptations, which are imparted through well-coordinated molecular mechanisms. New approaches, which include transcriptomics, genomics, proteomics, and metabolomics analyses, have opened the paths to understand such complex networks. This review sheds light on molecular mechanisms included in plant adaptive and defense responses during metal stress. It is focused on the entry of HMs into plants, its transport and accumulation, effects on the main physiological processes, gene expressions included in plant adaptive and defense responses during HM stress. Analysis of new data allowed the authors to conclude that the most important mechanism of HM tolerance is extracellular and intracellular HM sequestration. Organic anions (malate, oxalate, etc.) provide extracellular sequestration of HM ions. Intracellular HM sequestration depends not only on a direct binding mechanism with different polymers (pectin, lignin, cellulose, hemicellulose, etc.) or organic anions but also on the action of cellular receptors and transmembrane transporters. We focused on the functioning chloroplasts, mitochondria, and the Golgi complex under HM stress. The currently known molecular mechanisms of plant tolerance to the toxic effects of HMs are analyzed.

Plant Cadmium Resistance 2 (SaPCR2) Facilitates Cadmium Efflux in the Roots of Hyperaccumulator Sedum alfredii Hance

Hyperaccumulators are the preferred materials for phytoremediation. Sedum alfredii Hance is a cadmium (Cd) hyperaccumulator plant in China, although its detoxification mechanism remains unresolved. In our study, we cloned a gene belonging to the plant cadmium resistance (PCR) family, named SaPCR2, from the hyperaccumulating ecotype (HE) of S. alfredii. Sequence analysis indicated that SaPCR2 contained a cysteine-rich domain highly conserved in the PCR family and played an important role in Cd detoxification. Based on the relative quantitative results, SaPCR2 was highly expressed in the roots of HE S. alfredii, but not the shoots and Cd exposure did not significantly affect SaPCR2 expression. In contrast, the expression level of SaPCR2 was very low in plants of its non-hyperaccumulating ecotype (NHE). The subcellular localization of SaPCR2 in tobacco leaves and yeasts showed that SaPCR2 was localized on the plasma membrane and the expression of the SaPCR2 protein in a Zn/Cd-sensitive yeast Δzrc1 significantly increased its tolerance to Cd stress by decreasing the Cd content in cells. Heterologous expression of SaPCR2 in plants of both Arabidopsis thaliana and NHE S. alfredii significantly reduced the Cd levels in the roots, but not in the shoots. These results suggest that the overexpression of SaPCR2 in plants provides a route for Cd leak out of the root cells and protects the root cells against phytotoxicity of Cd stress. To the best of our knowledge, this is the first study of transporter-mediated root efflux of Cd in hyperaccumulator S. alfredii.

Identification of Durum Wheat Cultivars and Their Tetraploid Relatives with Low Cadmium Content

In this study, 71 durum wheat cultivars (Triticum durum Desf.), 22 emmer wheat (Triticum dicoccum L.) and 11 wild emmer (Triticum dicoccoides L.) genotypes were genetically characterized to determine the alleles associated with high cadmium (Cd) content. After genotypic characterization, 14 cultivars selected among all genotypes with low and high Cd content were phenotyped by a pot experiment to verify the genotypic data. Identification of 32 durum wheat, one emmer wheat and four wild emmer genotypes showed that they have alleles associated with high Cd content, while 68 genotypes of which 39 durum wheat, 21 emmer wheat and 7 wild emmer cultivars had alleles associated with low Cd content, respectively. Moreover, phenotypic data obtained from pot experiment were similar to the molecular data. To sum up, the marker successfully classified durum wheat cultivars into either high or low accumulators and these results can be safely used in breeding programs to improve new durum wheat cultivars with alleles associated with low Cd content. Due to routine use of phosphorus fertilizers in agricultural areas and other anthropogenic factors related to Cd toxicity, new durum wheat cultivars with low Cd content should be urgently developed for safe production of macaroni or other types of wheat products for human and animal consumption.

Impact of Pb on Chlamydomonas reinhardtii at Physiological and Transcriptional Levels

Trace elements stress is one of the most damaging abiotic stresses in environment. Nevertheless, the defense mechanism in microalgae remains poorly understood. In this study, physiological and molecular methods were performed to analyze the defense responses in green alga Chlamydomonas reinhardtii. It was speculated that the defense responses might mainly be due to the regulation of hormone signaling, indicating its potential role in alleviating the Pb toxicity besides other physiological and molecular defense responses like decrease in growth rate, chlorophyll content and photosynthesis efficiency, intensification of antioxidative mechanisms, regulation of transcription factors, trace elements chelation, and sequestration into vacuole via trace elements transporters. The sole differentially expressed ATP-binding cassette (ABC) transporters indicated that ABC transporters might play a very important role in the transport and relocation of Pb in C. reinhardtii. Additionally, our data provide the required knowledge for future investigations regarding Pb toxicity and defense mechanisms in algae, and detection of trace elements pollution in environment.

Exogenous abscisic acid (ABA) promotes cadmium (Cd) accumulation in Sedum alfredii Hance by regulating the expression of Cd stress response genes

Sedum alfredii Hance is a zinc (Zn) and cadmium (Cd) hyperaccumulator plant. However, the regulatory role of plant hormones in the Zn or Cd uptake and accumulation of S. alfredii remains unclear. In this work, the growth, Cd accumulation, abscisic acid (ABA) synthesis and catabolism, malonaldehyde (MDA) content, and transcriptional level of some Cd stress response genes under ABA and Cd co-treatment were investigated to reveal the impact of ABA on Cd resistance and Cd accumulation of S. alfredii. The results show that 0.2 mg/L ABA and 100 μmol/L Cd co-treatment enhanced Cd accumulation and growth in S. alfredii, whereas lower or higher ABA concentrations weaken or even reverse this effect, which was positively correlated with endogenous ABA content. The increase in endogenous ABA content might be the results of the increasing ABA synthetase activities and decreasing ABA lytic enzyme, which was induced by the application of 0.2 mg/L ABA under 100 μmol/L Cd treatment. Principal component analysis (PCA) indicated that ABA impacted the expression pattern of Cd stress response genes, which coincided with the Cd accumulation pattern in the shoots of S. alfredii. Cross-over analysis of partial least squares-discriminant analysis (PLS-DA) and correlation analysis indicated that HsfA4c, HMA4 expression in roots, and HMA2, HMA3, CAD, NAS expression in shoots were correlated with endogenous ABA, which suggests that endogenous ABA improves Cd resistance of seedlings, switches the root-to-shoot transporter from HMA2 to HMA4, and transports more Cd into apoplasts to promote Cd accumulation in the shoots of S. alfredii. Taken together, ABA plays an essential role not only in Cd resistance but also in Cd transport from root to shoot in S. alfredii under Cd stress.

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress

Cadmium (Cd) is a toxic heavy metal element. It is relatively easily absorbed by plants and enters the food chain, resulting in human exposure to Cd. Italian ryegrass (Lolium multiflorum Lam.), an important forage cultivated widely in temperate regions worldwide, has the potential to be used in phytoremediation. However, genes regulating Cd translocation and accumulation in this species are not fully understood. Here, we optimized PacBio ISO-seq and integrated it with RNA-seq to construct a de novo full-length transcriptomic database for an un-sequenced autotetraploid species. With the database, we identified 2367 differentially expressed genes (DEGs) and profiled the molecular regulatory pathways of Italian ryegrass with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis in response to Cd stress. Overexpression of a DEG LmAUX1 in Arabidopsis thaliana significantly enhanced plant Cd concentration. We also unveiled the complexity of alternative splicing (AS) with a genome-free strategy. We reconstructed full-length UniTransModels using the reference transcriptome, and 29.76% of full-length models had more than one isoform. Taken together, the results enhanced our understanding of the genetic diversity and complexity of Italian ryegrass under Cd stress and provided valuable genetic resources for its gene identification and molecular breeding.

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.

Transcriptomic analysis of Verbena bonariensis roots in response to cadmium stress

BACKGROUND

Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound adaptability, V. bonariensis could be adapted to this very situation. In our study, the Cd tolerance in V. bonariensis was analyzed as well as an overall analysis of transcriptome.

RESULTS

In this study, the tolerance of V. bonariensis to Cd stress was investigated in four aspects: germination, development, physiological changes, and molecular alterations. The results showed that as a non-hyperaccumulator, V. bonariensis did possess the Cd tolerance and the capability to concentration Cd. Under Cd stress, all 237, 866 transcripts and 191, 370 unigenes were constructed in the transcriptome data of V. bonariensis roots. The enrichment analysis of gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway revealed that differentially expressed genes (DEGs) under Cd stress were predominately related to cell structure, reactive oxygen species (ROS) scavenging system, chelating reaction and secondary metabolites, transpiration and photosynthesis. DEGs encoding lignin synthesis, chalcone synthase (CHS) and anthocyanidin synthase (ANS) were prominent in V. bonariensis under Cd stress. The expression patterns of 10 DEGs, validated by quantitative real-time polymerase chain reaction (qRT-PCR), were in highly accordance with the RNA-Sequence (RNA-Seq) results. The novel strategies brought by our study was not only benefit for further studies on the tolerance of Cd and functional genomics in V. bonariensis, but also for the improvement molecular breeding and phytoremediation.

Gene expression and biochemical response of giant reed under Ni and Cu stress

Giant reed (Arundo donax) has proved to be effective in detoxification, accumulation and tolerance of toxic metals. The present study explored the stress response of giant reed against Cu and Ni stress. The effect of metal stress was studied on dry weight, chlorophyll pigments antioxidant enzymes production and selected genes expression. The accumulation of heavy metals increased in a concentration-dependent manner and depicted toxicity symptoms in leaves beyond 75 mg/L of Cu or Ni. Oxidative stress was evident in giant reed under highest exposure of Ni and Cu which increased antioxidants activities (SOD, POD and CAT). It was observed that metal transport and detoxification were possible due to the expression of glutathione reductase, Natural Resistance-Associated Macrophage Protein (NRAMP) and Yellow Stripe-Like (YSL) genes. These insights into the genetic basis of a successful remediating plant species will be useful in understanding heavy metals tolerance in giant reed.

Inherent Metals of a Phytoremediation Plant Influence Its Recyclability by Hydrothermal Liquefaction

Plants used for phytoremediation of contaminated soil are often enriched in certain metals present in the soil. However, the role of the inherent metal content of the plants on their recycling by hydrothermal liquefaction (HTL) has not been considered in previous studies. The present study showed that Rhus chinensis plants grown in highly Pb-polluted soil can release inherent metals (such as Pb, K, Ca, Na, and Mg) into the HTL solution, further enhancing the production of formic and acetic acids and decreasing the yield of levulinic acid. Theoretical calculations using HTL reactions of model compounds showed that a low Pb content could enhance production of levulinic and formic acids via catalysis of the rehydration reaction for 5-(hydroxymethyl)furfural, while a high Pb content promoted the decomposition of levulinic acid to acetic acid. Fourier transform ion cyclotron resonance mass spectrometry analysis confirmed that Pb²⁺ preferentially promoted the depolymerization of macromolecular compounds with the lignin structure. In general, the inherent metals occurring in the phytoremediation plant influenced the production of organic acids during HTL recycling. Undoubtedly, the combination of phytoextraction and HTL reaction can present a practical pathway toward a sustainable soil remediation technology.

Elevated root nicotianamine concentrations are critical for Zn hyperaccumulation across diverse edaphic environments

The metallophyte Arabidopsis halleri thrives across an extremely broad edaphic range. Zn hyperaccumulation is found on soils differing in available Zn by up to six orders of magnitude, raising the question as to whether a common set of mechanisms confers this species-wide ability. Elevated root concentrations of the metal chelator nicotianamine due to strong constitutive expression of AhNAS2 are important for hyperaccumulation. In order to analyse the relevance of AhNAS2 under more natural conditions representing a range of metalliferous and nonmetalliferous habitats, we collected soil at eight different A. halleri sites and cultivated wild-type and AhNAS2-RNAi lines in these soils. AhNAS2 transcript abundance and root nicotianamine concentrations in wild-type plants were barely influenced by soil metal concentrations. The RNAi effect was fully expressed in different soils. Zn hyperaccumulation in AhNAS2-silenced lines was significantly reduced in seven soils. Root-to-shoot translocation of Cd, Mn, Cu, Ni, and Co was also affected by AhNAS2 silencing, albeit to a lower extent and less consistently. Leaf Fe levels were unaffected by AhNAS2 knockdown. Results demonstrate that elevated nicotianamine production in roots of A. halleri is a Zn hyperaccumulation factor regardless of the edaphic environment, that is, contributes to Zn hyperaccumulation in soils with contrasting Zn availability.

Differences of Cd uptake and expression of OAS and IRT genes in two varieties of ryegrasses

Pot experiment was conducted to study the difference of cadmium uptake and OAS and IRT genes' expression between the two ryegrass varieties under cadmium stress. The results showed that with the increase of cadmium levels, the dry weights of roots of the two ryegrass varieties, and the dry weights of shoots and plants of Abbott first increased and then decreased. When exposed to 75 mg kg^-1 Cd, the dry weights of shoot and plant of Abbott reached the maximum, which increased by 11.13 and 10.67% compared with the control. At 75 mg kg^-1 Cd, cadmium concentrations in shoot of the two ryegrass varieties were higher than the critical value of Cd hyperaccumulator (100 mg kg^-1), 111.19 mg kg^-1 (Bond), and 133.69 mg kg^-1 (Abbott), respectively. The OAS gene expression in the leaves of the two ryegrass varieties showed a unimodal curve, which was up to the highest at the cadmium level of 150 mg kg^-1, but fell back at high cadmium levels of 300 and 600 mg kg^-1. The OAS gene expression in Bond and Abbott roots showed a bimodal curve. The OAS gene expression in Bond root and Abbott stem mainly showed a unimodal curve. The expression of IRT genes family in the leaves of ryegrass varieties was basically in line with the characteristics of unimodal curve, which was up to the highest at cadmium level of 75 or 150 mg kg^-1, respectively. The IRT expression in the ryegrass stems showed characteristics of bimodal and unimodal curves, while that in the roots was mainly unimodal. The expression of OAS and IRT genes was higher in Bond than that in Abbott due to genotype difference between the two varieties. The expression of OAS and IRT was greater in leaves than that in roots and stems. Ryegrass tolerance to cadmium can be increased by increasing the expression of OAS and IRT genes in roots and stems, and transfer of cadmium from roots and stems to the leaves can be enhanced by increasing expression OAS and IRT in leaves.

Abscisic acid-mediated modifications of radial apoplastic transport pathway play a key role in cadmium uptake in hyperaccumulator Sedum alfredii

Abscisic acid (ABA) is a key phytohormone underlying plant resistance to toxic metals. However, regulatory effects of ABA on apoplastic transport in roots and consequences for uptake of metal ions are poorly understood. Here, we demonstrate how ABA regulates development of apoplastic barriers in roots of two ecotypes of Sedum alfredii and assess effects on cadmium (Cd) uptake. Under Cd treatment, increased endogenous ABA level was detected in roots of nonhyperaccumulating ecotype (NHE) due to up-regulated expressions of ABA biosynthesis genes (SaABA2, SaNCED), but no change was observed in hyperaccumulating ecotype (HE). Simultaneously, endodermal Casparian strips (CSs) and suberin lamellae (SL) were deposited closer to root tips of NHE compared with HE. Interestingly, the vessel-to-CSs overlap was identified as an ABA-driven anatomical trait. Results of correlation analyses and exogenous applications of ABA/Abamine indicate that ABA regulates development of both types of apoplastic barriers through promoting activities of phenylalanine ammonialyase, peroxidase, and expressions of suberin-related genes (SaCYP86A1, SaGPAT5, and SaKCS20). Using scanning ion-selected electrode technique and PTS tracer confirmed that ABA-promoted deposition of CSs and SL significantly reduced Cd entrance into root stele. Therefore, maintenance of low ABA levels in HE minimized deposition of apoplastic barriers and allowed maximization of Cd uptake via apoplastic pathway.

Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress

Background

The herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family's responses to heavy metal-stress conditions.

Methods

Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl₂ for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd.

Results

We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed.

Conclusion

Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved domain, motif and expression profiling of the GELP family under Cd-stress conditions. SaGLIP8 could increase Cd tolerance and accumulation in yeast. These results indicated the roles of GELPs in plant responses to heavy metal exposure and provides a theoretical basis for further studies of the SaGELP family's functions.

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.

Transcriptome analysis providing novel insights for Cd-resistant tall fescue responses to Cd stress

Cadmium (Cd) is a severely toxic heavy metal and environmental pollutant. Tall fescue is a cold season turf grass which has high resistance to Cd as well as the ability to enrich it. To investigate the molecular mechanism underlying the adaptability of tall fescue to Cd stress, RNA-Seq was used to examine Cd stress responses of tall fescue at a transcriptional level. A total of 12 cDNA libraries were constructed from the total RNA of roots or leaves of tall fescue with or without Cd treatments. A total of 2594 (1768 up- and 826 down-regulated) differentially expressed genes (DEGs) were detected in the roots of Cd-stressed tall fescue compared with control roots (R_cd vs R_ck), while only 52 (29 up- and 23 down-regulated) DEGs were found in the leaves of Cd-stressed plants versus the controls (L_cd vs L_ck). The genes encoding glutathione S-transferase (GST), transporter proteins including the ABC transporter, ZRT/IRT-like protein, potassium transporter/channel, nitrate transporter, putative iron-phytosiderophore transporter, copper-transporting ATPase or transporter and multidrug and toxic compound extrusion (MATE) proteins, and numerous transcription factors were found to be significantly induced in Cd-treated roots. In addition, pathogenesis/disease-related gene mRNAs were accumulated in Cd-treated roots of tall fescue. Furthermore, the significantly enriched KEGG pathways in roots were related to 'Glutathione metabolism', 'Ribosome', 'alpha-Linolenic acid metabolism', 'Diterpenoid biosynthesis', 'Sulfur metabolism', 'Phenylpropanoid biosynthesis', 'Protein processing in endoplasmic reticulum', 'Protein export' and 'Nitrogen metabolism'. The study provides novel insights for further understanding the molecular mechanisms of tall fescue responses to Cd stress.

Comparative RNA-seq analysis of nickel hyperaccumulating and non-accumulating populations of Senecio coronatus (Asteraceae)

Most metal hyperaccumulating plants accumulate nickel, yet the molecular basis of Ni hyperaccumulation is not well understood. We chose Senecio coronatus to investigate this phenomenon as this species displays marked variation in shoot Ni content across ultramafic outcrops in the Barberton Greenstone Belt (South Africa), thus allowing an intraspecific comparative approach to be employed. No correlation between soil and shoot Ni contents was observed, suggesting that this variation has a genetic rather than environmental basis. This was confirmed by our observation that the accumulation phenotype of plants from two hyperaccumulator and two non-accumulator populations was maintained when the plants were grown on a soil mix from these four sites for 12 months. We analysed the genetic variation among 12 serpentine populations of S. coronatus, and used RNA-seq for de novo transcriptome assembly and analysis of gene expression in hyperaccumulator versus non-accumulator populations. Genetic analysis revealed the presence of hyperaccumulators in two well supported evolutionary lineages, indicating that Ni hyperaccumulation may have evolved more than once in this species. RNA-Seq analysis indicated that putative homologues of transporters associated with root iron uptake in plants are expressed at elevated levels in roots and shoots of hyperaccumulating populations of S. coronatus from both evolutionary lineages. We hypothesise that Ni hyperaccumulation in S. coronatus may have evolved through recruitment of these transporters, which play a role in the iron-deficiency response in other plant species.

Ectopic expression of SaNRAMP3 from Sedum alfredii enhanced cadmium root-to-shoot transport in Brassica juncea

SaNRAMP3 gene cloned from a Zn/Cd hyperaccumulator Sedum alfredii was ectopicly expressed in Brassica juncea, a fast-growing and high-biomass crop plant. In a tissue culture experiment, transgenic plants were grown on MS medium with 0, 25, 50, 100, 200 μM Cd. It was shown that, at the same Cd treatment, the Cd tolerance of transgenic plants had no significant difference with those of wild-type plants (WT). However, the shoot Cd content and accumulation were improved significantly while the root Cd content and accumulation were descended significantly by SaNRAMP3 gene expression, which obviously enhanced the Cd root-to-shoot translocation factor (TF). In the hydroponic experiment, plants were cultured in nutrition solution with 0, 2.5, 25 μM Cd. Data showed that the Cd tolerance of transgenic plants had no significant difference with that of WT under the same Cd exposure. Whereas, the shoot Cd content and accumulation was increased 1.43-1.81 times and the TF was enhanced 3.09-3.51 times by SaNRAMP3 gene expression. Those results indicated that ectopic expression of SaNRAMP3 in B. juncea didn't lead to Cd sensitivity, but enhanced Cd root-to-shoot transport, so that increased shoot Cd accumulation. This study provided a possibility to improve phytoextraction efficiency of heavy metal through gene engineering.

Identification of differentially accumulated proteins involved in regulating independent and combined osmosis and cadmium stress response in Brachypodium seedling roots

In this study, we aimed to identify differentially accumulated proteins (DAPs) involved in PEG mock osmotic stress, cadmium (Cd²⁺) stress, and their combined stress responses in Brachypodium distachyon seedling roots. The results showed that combined PEG and Cd²⁺ stresses had more significant effects on Brachypodium seedling root growth, physiological traits, and ultrastructures when compared with each individual stress. Totally, 106 DAPs were identified that are responsive to individual and combined stresses in roots. These DAPs were mainly involved in energy metabolism, detoxification and stress defense and protein metabolism. Principal component analysis revealed that DAPs from Cd²⁺ and combined stress treatments were grouped closer than those from osmotic stress treatment, indicating that Cd²⁺ and combined stresses had more severe influences on the root proteome than osmotic stress alone. Protein-protein interaction analyses highlighted a 14-3-3 centered sub-network that synergistically responded to osmotic and Cd²⁺ stresses and their combined stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 14 key DAP genes revealed that most genes showed consistency between transcriptional and translational expression patterns. A putative pathway of proteome metabolic changes in Brachypodium seedling roots under different stresses was proposed, which revealed a complicated synergetic responsive network of plant roots to adverse environments.

Genome-Wide Identification of MicroRNAs in Response to Cadmium Stress in Oilseed Rape (Brassica napus L.) Using High-Throughput Sequencing

MicroRNAs (miRNAs) have important roles in regulating stress-response genes in plants. However, identification of miRNAs and the corresponding target genes that are induced in response to cadmium (Cd) stress in Brassica napus remains limited. In the current study, we sequenced three small-RNA libraries from B. napus after 0 days, 1 days, and 3 days of Cd treatment. In total, 44 known miRNAs (belonging to 27 families) and 103 novel miRNAs were identified. A comprehensive analysis of miRNA expression profiles found 39 differentially expressed miRNAs between control and Cd-treated plants; 13 differentially expressed miRNAs were confirmed by qRT-PCR. Characterization of the corresponding target genes indicated functions in processes including transcription factor regulation, biotic stress response, ion homeostasis, and secondary metabolism. Furthermore, we propose a hypothetical model of the Cd-response mechanism in B. napus. Combined with qRT-PCR confirmation, our data suggested that miRNAs were involved in the regulations of TFs, biotic stress defense, ion homeostasis and secondary metabolism synthesis to respond Cd stress in B. napus.

Global Picture of Protein Regulation in Response to Dibutyl Phthalate (DBP) Stress of Two Brassica parachinensis Cultivars Differing in DBP Accumulation

iTRAQ analysis was used to map the proteomes of two Brassica parachinensis cultivars that differed in dibutyl phthalate (DBP) accumulation. A total of 5699 proteins were identified to obtain 152 differentially regulated proteins, of which 64 and 48 were specific to a high- and a low-DBP-accumulation cultivar, respectively. Genotype-specific biological processes were involved in coping with DBP stress, accounting for the variation in DBP tolerance and accumulation. Formation of high DBP accumulation in B. parachinensis might attribute to the more effective regulation of protein expression in physiology and metabolism, including (a) enhanced cell wall biosynthesis and modification, (b) better maintenance of photosynthesis and energy balance, (c) greatly improved total capacity for antioxidation and detoxification, and (d) enhanced cellular transport and signal transduction. Our novel findings contribute to a global picture of DBP-induced alterations of protein profiles in crops and provide valuable information for the development of molecular-assisted breeds of low-accumulation cultivars.

Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24

In this work, we genetically characterized the function of Arabidopsis thaliana, LONGIFOLIA (LNG1), LNG2, LNG3, LNG4, their contribution to regulate vegetative architecture in plant. We used molecular and biophysical approaches to elucidate a gene function that regulates vegetative architecture, as revealed by the leaf phenotype and later effects on flowering patterns in Arabidopsis loss-of-function mutants. As a result, LNG genes play an important role in polar cell elongation by turgor pressure controlling the activation of XTH17 and XTH24. Plant vegetative architecture is related to important traits that later influence the floral architecture involved in seed production. Leaf morphology is the primary key trait to compose plant vegetative architecture. However, molecular mechanism on leaf shape determination is not fully understood even in the model plant A. thaliana. We previously showed that LONGIFOLIA (LNG1) and LONGIFOLIA2 (LNG2) genes regulate leaf morphology by promoting longitudinal cell elongation in Arabidopsis. In this study, we further characterized two homologs of LNG1, LNG3, and LNG4, using genetic, biophysical, and molecular approaches. Single loss-of-function mutants, lng3 and lng4, do not show any phenotypic difference, but mutants of lng quadruple (lngq), and lng1/2/3 and lng1/2/4 triples, display reduced leaf length, compared to wild type. Using the paradermal analysis, we conclude that the reduced leaf size of lngq is due to decreased cell elongation in the direction of longitudinal leaf growth, and not decreased cell proliferation. This data indicate that LNG1/2/3/4 are functionally redundant, and are involved in polar cell elongation in Arabidopsis leaf. Using a biophysical approach, we show that the LNGs contribute to maintain high turgor pressure, thus regulating turgor pressure-dependent polar cell elongation. In addition, gene expression analysis showed that LNGs positively regulate the expression of the cell wall modifying enzyme encoded by a multi-gene family, xyloglucan endotransglucosylase/hydrolase (XTH). Taking all of these together, we propose that LNG related genes play an important role in polar cell elongation by changing turgor pressure and controlling the activation of XTH17 and XTH24.

Conceptualizing plant systems evolution

Organisms inhabiting extreme environments are emerging models in systems evolution, enabling us to identify the molecular alterations effecting major phenotypic divergence through comparative approaches. Here I discuss possible physiological mechanisms underlying evolutionary adaptations to extreme environments both theoretically and in relation to experimental observations. Reasoning leads me to the 'conserved steady-state' hypothesis of evolutionary adaptation: Between closely related plants adapted to differently composed soils, the homeostatically controlled steady-state set point cytosolic (buffered) concentrations of mineral ions are conserved. Subsequently, I compare molecular alterations expected to contribute to physiological adaptations with our present knowledge. Key roles of enhanced gene product dosage in plant evolutionary adaptations question the widespread stimulus response-centric paradigm. As a broader implication, co-regulation networks can lack decisive functional network elements. With this article, I hope to stimulate a discussion across research fields and provide an initial conceptual framework for future experimental testing and for quantitative modelling.

The Response of Duckweed (Lemna minor L.) Roots to Cd and Its Chemical Forms

The response of duckweed (Lemna minor L.) roots to Cd and its chemical forms was investigated. The relative root growth rate and concentrations of Cd and its different chemical forms in the root, that is, ethanol-extractable (FE-Cd), HCl-extractable (FHCl-Cd), and residual fractions (Fr-Cd), were quantified. Weibull model was used to unravel the regression between the relative root elongation (RRL) with chemical forms of Cd. Parameters assessed catalase (CAT), peroxidases (POD), and superoxide dismutase (SOD), as well as malondialdehyde (MDA) and total antioxidant capacity (A-TOC). Our results show that both the relative root growth rate and relative frond number were affected by Cd concentrations. The chemical forms of Cd were influenced by Cd content in the medium. Relative root elongation (RRL) showed a significant correlation with chemical forms of Cd. Additionally, POD and SOD increased at lower Cd concentrations followed by a decrease at higher Cd concentrations (at more than 5 μM Cd). Moreover, MDA and A-TOC increased and CAT decreased with increasing Cd exposure. Furthermore, CAT showed a significant correlation with FHCl-Cd. Taken together, it can be concluded that the chemical forms of Cd are statistically significant predictors of Cd toxicity to duckweed and to the other similar aquatic plants.

The Effects of the Endophytic Bacterium Pseudomonas fluorescens Sasm05 and IAA on the Plant Growth and Cadmium Uptake of Sedum alfredii Hance

Endophytic bacteria have received attention for their ability to promote plant growth and enhance phytoremediation, which may be attributed to their ability to produce indole-3-acetic acid (IAA). As a signal molecular, IAA plays a key role on the interaction of plant and its endomicrobes. However, the different effects that endophytic bacteria and IAA may have on plant growth and heavy metal uptake is not clear. In this study, the endophytic bacterium Pseudomonas fluorescens Sasm05 was isolated from the stem of the zinc (Zn)/cadmium (Cd) hyperaccumulator Sedum alfredii Hance. The effects of Sasm05 and exogenous IAA on plant growth, leaf chlorophyll concentration, leaf Mg²⁺-ATPase and Ca²⁺-ATPase activity, cadmium (Cd) uptake and accumulation as well as the expression of metal transporter genes were compared in a hydroponic experiment with 10 μM Cd. The results showed that after treatment with 1 μM IAA, the shoot biomass and chlorophyll concentration increased significantly, but the Cd uptake and accumulation by the plant was not obviously affected. Sasm05 inoculation dramatically increased plant biomass, Cd concentration, shoot chlorophyll concentration and enzyme activities, largely improved the relative expression of the three metal transporter families ZRT/IRT-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) and heavy metal ATPase (HMA). Sasm05 stimulated the expression of the SaHMAs (SaHMA2, SaHMA3, and SaHMA4), which enhanced Cd root to shoot translocation, and upregulated SaZIP, especially SaIRT1, expression to increase Cd uptake. These results showed that although both exogenous IAA and Sasm05 inoculation can improve plant growth and photosynthesis, Sasm05 inoculation has a greater effect on Cd uptake and translocation, indicating that this endophytic bacterium might not only produce IAA to promote plant growth under Cd stress but also directly regulate the expression of putative key Cd uptake and transport genes to enhance Cd accumulation of plant.

De novo characterization of the Iris lactea var. chinensis transcriptome and an analysis of genes under cadmium or lead exposure

Iris lactea var. chinensis (I. lactea var. chinensis) is tolerant to accumulations of cadmium (Cd) and lead (Pb). In this study, the transcriptome of I. lactea var. chinensis was investigated under Cd or Pb stresses. Using the gene ontology database, 31,974 unigenes were classified into biological process, cellular component and molecular function. In total, 13,132 unigenes were involved in enriched Encyclopedia of Genes and Genomes (KEGG) metabolic pathways, and the expression levels of 5904 unigenes were significantly changed after exposure to Cd or Pb stresses. Of these, 974 were co-up-regulated and 1281 were co-down-regulated under the two stresses. The transcriptome expression profiles of I. lactea var. chinensis under Cd or Pb stresses obtained in this study provided a resource for identifying common mechanisms in the detoxification of different heavy metals. Furthermore, the identified unigenes may be used for the genetic breeding of heavy-metal tolerant plants.

Transcriptome analysis of Phytolacca americana L. in response to cadmium stress

Phytolacca americana L. (pokeweed) has metal phytoremediation potential, but little is known about its metal accumulation-related genes. In this study, the de novo sequencing of total RNA produced 53.15 million reads covering 10.63 gigabases of transcriptome raw data in cadmium (Cd)-treated and untreated pokeweed. Of the 97,502 assembled unigenes, 42,197 had significant matches in a public database and were annotated accordingly. An expression level comparison between the samples revealed 1515 differentially expressed genes (DEGs), 923 down- and 592 up-regulated under Cd treatment. A KEGG pathway enrichment analysis of DEGs revealed that they were involved in 72 metabolism pathways, with photosynthesis, phenylalanine metabolism, ribosome, phenylpropanoid biosynthesis, flavonoid biosynthesis and carbon fixation in photosynthetic organisms containing 24, 18, 72, 14, 7 and 15 genes, respectively. Genes related to heavy metal tolerance, absorption, transport and accumulation were also identified, including 11 expansins, 8 nicotianamine synthases, 6 aquaporins, 4 ZRT/IRT-like proteins, 3 ABC transporters and 3 metallothioneins. The gene expression results of 12 randomly selected DEGs were validated using quantitative real-time PCR, and showed different response patterns to Cd in their roots, stems and leaves. These results may be helpful in increasing our understanding of heavy metal hyperaccumulators and in future phytoremediation applications.

Transcriptome Comparison Reveals the Adaptive Evolution of Two Contrasting Ecotypes of Zn/Cd Hyperaccumulator Sedum alfredii Hance

Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE. We used a branch-site model to identify 18 divergent orthologous genes and 57 conserved orthologous genes of S. alfredii Hance. The divergent orthologous genes were mainly involved in the transcription and translation processes, protein metabolism process, calcium (Ca²⁺) pathway, stress response process and signal transduction process. To the best of our knowledge, this is the first study to use RNA-seq to compare the genetic evolution of hyperaccumulating and non-hyperaccumulating plants from the same species. In addition, this study made the sole concrete for further studies on molecular markers and divergent orthologous genes to depict the evolution process and formation of the hyperaccumulation and hypertolerance traits in S. alfredii Hance.

The effects of endophytic bacterium SaMR12 on Sedum alfredii Hance metal ion uptake and the expression of three transporter family genes after cadmium exposure

A hydroponic experiment was conducted to investigate the effects of an endophytic bacterium SaMR12 on Sedum alfredii Hance metal ion accumulation, chlorophyll concentration, and the expression of three metal transporter families, zinc-regulated transporters, iron-regulated transporter-like protein (ZIP); natural resistance-associated macrophage protein; and heavy metal ATPase (HMA) at different Cd treatment levels. The results showed that at relatively low Cd conditions (≤25 μM), SaMR12 demonstrated a 19.5-27.5% increase in Fe, a 46.7-90.7% increase in Zn, and a 7.9-43.7% increase in Cu content in the shoot and elevated expression of SaIRT1, SaZIP3, SaHMA2, and SaNramp3 in the shoot and SaZIP1, SaHMA2, SaNramp1, and SaNramp3 in the root. At high Cd conditions (100 and 400 μM), SaMR12 demonstrated a 16.4-18.5% increase in leaf chlorophyll concentration, a 18.9-23.2% increase in Fe, and a 15.4-17.5% increase in Mg content in the shoot and elevated expression of SaZIP3, SaNramp6, SaHMA2, and SaHMA3 in the shoot and SaZIP3, SaNarmp1, SaNarmp3, and SaNarmp6 in the root. These results indicated that SaMR12 can elevate essential metal ion uptake and regulate the expression of transport genes to promote plant growth and enhance Cd tolerance and uptake to improve Cd accumulation up to 118-130%.

Enhanced Cd extraction of oilseed rape (Brassica napus) by plant growth-promoting bacteria isolated from Cd hyperaccumulator Sedum alfredii Hance

Four plant growth-promoting bacteria (PGPB) were used as study materials, among them two heavy metal-tolerant rhizosphere strains SrN1 (Arthrobacter sp.) and SrN9 (Bacillus altitudinis) were isolated from rhizosphere soil, while two endophytic strains SaN1 (Bacillus megaterium) and SaMR12 (Sphingomonas) were identified from roots of the cadmium (Cd)/zinc (Zn) hyperaccumulator Sedum alfredii Hance. A pot experiment was carried out to investigate the effects of these PGPB on plant growth and Cd accumulation of oilseed rape (Brassica napus) plants grown on aged Cd-spiked soil. The results showed that the four PGPB significantly boosted oilseed rape shoot biomass production, improved soil and plant analyzer development (SPAD) value, enhanced Cd uptake of plant and Cd translocation to the leaves. By fluorescent in situ hybridization (FISH) and green fluorescent protein (GFP), we demonstrated the studied S. alfredii endophytic bacterium SaMR12 were able to colonize successfully in the B. napus roots. However, all four PGPB could increase seed Cd accumulation. Due to its potential to enhance Cd uptake by the plant and to restrict Cd accumulation in the seeds, SaMR12 was selected as the most promising microbial partner of B. napus when setting up a plant-microbe fortified remediation system.

Transcription Factors PvERF15 and PvMTF-1 Form a Cadmium Stress Transcriptional Pathway

In plants, cadmium (Cd)-responsive transcription factors are key downstream effectors of Cd stress transcriptional pathways, which are capable of converging Cd stress signals through triggering the expression of Cd detoxification genes. However, the upstream transcriptional regulatory pathways that modulate their responses to Cd are less clear. Previously, we identified the bean (Phaseolus vulgaris) METAL RESPONSE ELEMENT-BINDING TRANSCRIPTION FACTOR1 (PvMTF-1) that responds to Cd and confers Cd tolerance in planta. Here, we demonstrate an upstream transcriptional regulation of the PvMTF-1 response to Cd Using a yeast one-hybrid system, we cloned the bean ETHYLENE RESPONSE FACTOR15 (PvERF15) that binds to the PvMTF-1 promoter. PvERF15 was strongly induced by Cd stress, and its overexpression resulted in the up-regulation of PvMTF-1 DNA-protein interaction assays further revealed that PvERF15 binds directly to a 19-bp AC-rich element in the PvMTF-1 promoter. The AC-rich element serves as a positive element bound by PvERF15 to activate gene expression. More importantly, knockdown of PvERF15 by RNA interference resulted in reduced Cd-induced expression of PvMTF-1PvERF15 seems to be involved in Cd tolerance, since knockdown of PvERF15 by RNA interference in bean leaf discs decreased Cd tolerance in a transient assay. Since PvERF15 is a component of the Cd stress transcriptional pathway in beans and PvMTF-1 is one of its downstream targets, our findings provide a PvERF15/PvMTF-1 transcriptional pathway and thereby contribute to the understanding of Cd stress transcriptional regulatory pathways in plants.

Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing

Perennial ryegrass (Lolium perenne) is one of the most widely used forage and turf grasses in the world due to its desirable agronomic qualities. However, as a cool-season perennial grass species, high temperature is a major factor limiting its performance in warmer and transition regions. In this study, a de novo transcriptome was generated using a cDNA library constructed from perennial ryegrass leaves subjected to short-term heat stress treatment. Then the expression profiling and identification of perennial ryegrass heat response genes by digital gene expression analyses was performed. The goal of this work was to produce expression profiles of high temperature stress responsive genes in perennial ryegrass leaves and further identify the potentially important candidate genes with altered levels of transcript, such as those genes involved in transcriptional regulation, antioxidant responses, plant hormones and signal transduction, and cellular metabolism. The de novo assembly of perennial ryegrass transcriptome in this study obtained more total and annotated unigenes compared to previously published ones. Many DEGs identified were genes that are known to respond to heat stress in plants, including HSFs, HSPs, and antioxidant related genes. In the meanwhile, we also identified four gene candidates mainly involved in C₄ carbon fixation, and one TOR gene. Their exact roles in plant heat stress response need to dissect further. This study would be important by providing the gene resources for improving heat stress tolerance in both perennial ryegrass and other cool-season perennial grass plants.