Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua

Gene-guided identifications of a structure-chimeric cyclotide viphi I from Viola philippica: Potential functions against cadmium and nematodes

The cyclic peptides, cyclotides, are identified mostly with 29-31-aa (amino acid residues) but rarely with ≥ 34-aa in plants. Viola philippica is a well-known medicinal plant but a rare metallophyte with cyclotides. A hypothesis was hence raised that the potential novel 34-aa cyclotide of Viola philippica would clearly broaden the structural and functional diversities of plant cyclotides. After homology-cloning the cyclotide precursor gene of VpCP5, a 34-aa cyclotide (viphi I) was identified to be larger than 22 other known cyclotides in V. philippica. It had a chimeric primary structure, due to its unusual loop structures (8 residues in loop 2 and 6 residues in loop 5) and aa composition (3 E and 5 R), by using phylogenetic analyses and an in-house cyclotide analysis tool, CyExcel_V1. A plasmid pCYC-viphi_I and a lab-used recombinant process were specially constructed for preparing viphi I. Typically, 0.12 or 0.25 mg ml-1 co-exposed viphi I could significantly remain cell activities with elevating Cd2+-exposed doses from 10-8 to 10-6 mol l-1 in MCF7 cells. In the model nematode Caenorhabditis elegans, IC50 values of viphi I to inhibit adult ratios and to induce death ratios, were 184.7 and 585.9 µg ml-1, respectively; the median lifespan of adult worms decreased from 14 to 2 d at viphi I doses ranging from 0.05 to 2 mg ml-1. Taken together, the newly identified viphi I exhibits functional potentials against cadmium and nematodes, providing new insights into structural and functional diversity of chimeric cyclotides in plants.

The involvement of cyclotides in the heavy metal tolerance of Viola spp

The Violaceae family is rich in metal-tolerant species and species producing cyclic peptides (cyclotides) that are linked to the resistance to biotic factors. Plants that inhabit areas polluted with heavy metals have developed various mechanisms of tolerance. To test the role of cyclotides in protection against abiotic factors, including heavy metals, cell suspension cultures of Viola species/genotypes (V. lutea ssp. westfalica, V. tricolor, V. arvensis, and V. uliginosa), representing different levels of tolerance to heavy metals (from the most tolerant-MET to the least tolerant populations/species-NMET), were used. The relative abundances of the cyclotides in the control, untreated cell suspensions of all the selected species/genotypes, and cells treated with Zn or Pb (200 µM or 2000 µM) for 24 h or 72 h were determined via MALDI-MS. Transmission electron microscopy with X-ray microanalysis was used to detect putative co-localization of the cyclotides with Zn or Pb in the cells of V. tricolor treated with the highest concentration of heavy metals for 72 h. Cyclotide biosynthesis was dependent on the type of heavy metal and its concentration, time of treatment, plant species, and population type (MET vs. NMET). It was positively correlated with the level of tolerance of particular Viola species. The increased production of cyclotides was observed in the cells of metallophyte species, mostly in Zn-treated cells. The nonmetallophyte-V. uliginosa presented a decrease in the production of cyclotides independent of the dose and duration of the metal treatment. Cyclotides co-localized with Pb more evidently than with Zn, suggesting that cyclotides have heavy metal affinity. V. lutea ssp. westfalica transcriptome mining yielded 100 cyclotide sequences, 16 known and 84 novel named viwe 1-84. These findings support the hypothesis that cyclotides are involved in certain mechanisms of plant tolerance to heavy metals.

A comparative study on cadmium tolerance and applicability of two Solanum lycopersicum L. cultivars

Solanum lycopersicum L. can be classified into low Cd-accumulating and high Cd-accumulating types based on their accumulation characteristics of cadmium (Cd). There are many common S. lycopersicum varieties available in the market, but their specific Cd tolerance and enrichment abilities are not well understood. This article uses two S. lycopersicum cultivars, Yellow Cherry and Yellow Pearl, as experimental materials. The experimental method of soil pot planting was adopted, and Cd concentrations in the soil were added at 0, 0.6, 1.5, 2.5, 5, and 10 mg/kg. The changes in Cd content, biomass, photosynthetic pigment content, and photosynthetic parameters of the two S. lycopersicum cultivars were analyzed to screen for low-accumulation S. lycopersicum cultivars. The results showed that S. lycopersicum are Cd-sensitive plants. The Cd accumulation, photosynthetic parameters, and other basic indicators of Yellow Cherry basically showed significant differences when the soil Cd concentration was 0.6 mg/kg, and the biomass showed significant differences when the soil Cd concentration was 1.5 mg/kg. Except for the Cd accumulation in the roots and leaves of Yellow Pearl, which showed significant differences at a soil Cd concentration of 0.6 mg/kg, the other indicators basically showed significant differences when the soil Cd concentration was 1.5 mg/kg. When the soil Cd concentration was 0.6 mg/kg, the Cd accumulation in the fruit of Yellow Pearl was 0.04 mg/kg, making it a low-accumulation S. lycopersicum variety suitable for promoting cultivation in Cd-contaminated soil at 0.6 mg/kg. In conclusion, the Cd accumulation in the fruit of Yellow Pearl is significantly lower than that of Yellow Cherry and even below the Cd limit value for fresh vegetables specified in GB2762-2017. Therefore, Yellow Pearl can be grown as edible crops in soils with Cd concentrations ≤0.6 mg/kg. Furthermore, Yellow Cherry demonstrate strong Cd tolerance and can be used for the remediation of Cd-contaminated soils.

Ectopic expression of SaCTP3 from the hyperaccumulator Sedum alfredii in sorghum increases Cd accumulation for phytoextraction

The Cd tolerance protein SaCTP3, which responds to Cd stress, was identified in Sedum alfredii; however, how to improve the efficiency of phytoremediation of Cd-contaminated soil using the CTP gene remains unknown. In this study, the phytoremediation potential of SaCTP3 of Sedum alfredii was identified. In the yeast Cd-sensitive strain Δycf1 overexpressing SaCTP3, the accumulation of Cd was higher than that in the Δycf1 strain overexpressing an empty vector. Transgenic sorghum plants overexpression SaCTP3 were further constructed to verify the function of SaCTP3. Compared to wild-type plants, the SaCTP3-overexpressing lines exhibited higher Cd accumulation under 500 μM Cd conditions. The average Cd content inSaCTP3-overexpressing plants is more than four times higher than that of WT plants. This was accompanied by an enhanced ability to scavenge ROS, as evidenced by the significantly increased activities of peroxidase, catalase, and superoxide dismutase in response to Cd stress. Pot experiments further demonstrated that SaCTP3 overexpression resulted in improved soil Cd scavenging and photosynthetic abilities. After 20 days of growth, the average Cd content in the soil planted with SaCTP3-overexpressing sorghum decreased by 19.4%, while the residual Cd content in the soil planted with wild-type plants was only reduced by 5.4%. This study elucidated the role of SaCTP3 from S.alfredii, highlighting its potential utility in genetically modifying sorghum for the effective phytoremediation of Cd.

Broadening the host range and genetic diversity of waikaviruses

Waikaviruses are monopartite, positive sense, single-stranded RNA viruses that cause economically important plant diseases. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. The present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD) identified 22 putative new waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features was identified in a wheat transcriptome. Other significant findings of the study include identification of a new waikavirus in a library derived from diseased water chestnut sample wherein a caulimovirus was reported, prediction of coiled-coils in hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses. The study not only reiterates the importance of DDVD in unveiling hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.

Bivalent copper ions presence triggers removal and homeostatic mechanisms in the metal-resistant microorganism Apiotrichum loubieri M12

Microorganisms, especially those habiting mining environments, are of great importance for the retention of toxic metals in the environment. This work aimed to isolate a copper removing-microorganism from sediments of an Acid Mine Drainage-affected environment and to study the cellular responses trigger by metal presence. Apiotrichum loubieri M12 was able to tolerate and remove Cu(II) from liquid culture media, reaching a 30-35% removal capacity when it was exposed to 40 μg mL^-1 Cu(II) after 48 h. Analysis of the biomass exposed to the metal through SEM-EDS showed copper presence on the cell surface and variations in the proportion of other biomass constituent elements. Proteomics revealed that the presence of Cu(II) induces differential expression of intracellular proteins involved in a wide variety of metabolic processes. Interestingly, a specific response to the metal was detected in cell-free supernatants, in which copper binding proteins were identified. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The microorganism responds not only by adjusting intracellular protein expression, but also by adjusting expression of proteins in the extracellular space.

Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil

High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.

Integrated physiologic and proteomic analysis of Stropharia rugosoannulata mycelia in response to Cd stress

Soil Cd pollution seriously threatens environment and human health. Due to its ability to absorb and accumulate Cd in mycelia, Stropharia rugosoannulata could be a potential candidate for bioremediation of Cd-contaminated soils; however, the response mechanism of mycelia to Cd stress is still unclear. In this study, the physiologic and proteomic differences of S. rugosoannulata mycelia under 0.2 mg/L (low) and 2 mg/L (high) Cd stress were investigated. The results showed that Cd accumulation and mycelial growth inhibition exhibited a concentration-depended trend. Analysis of antioxidant system indicated that SOD, GR, GSH, GSSG and ASA played key roles in resisting the toxic effects of Cd. Via proteome analysis, 24 and 267 differentially expressed proteins (DEPs) were observed under low and high Cd stress, respectively. GO and KEGG analysis found that the mycelial growth inhibition might due to the down-regulation of some DEPs involved in "valine, leucine and isoleucine biosynthesis" and "tyrosine metabolism"; the certain tolerance to high Cd stress might attribute to the regulation of DEPs referred to energy metabolism and antioxidant system-related pathways, maintaining cellular energy homeostasis and removing ROS. These results provide a theoretical basis for further elucidation of response mechanisms in S. rugosoannulata to Cd stress.

Transcriptome alterations of radish shoots exposed to cadmium can be interpreted in the context of leaf senescence

Till now few transcriptome studies have described shoot responses of heavy metal (HM)-sensitive plants to excess Cd and still a unifying model of Cd action is lacking. Using RNA-seq technique, the transcriptome responses of radish (Raphanus sativus L.) leaves to Cd stress were investigated in plants raised hydroponically under control and 5.0 mg L^-1 Cd. The element was mainly accumulated in roots and led to declined biomass and photosynthetic pigments, increased H₂O₂ and lipid peroxidation, and the accumulation of sugars, protein thiols, and phytochelatins. Out of 524 differentially expressed genes (DEGs), 244 and 280 upregulated and downregulated ones were assigned to 82 and 115 GO terms, respectively. The upregulated DEGs were involved in osmotic regulation, protein metabolism, chelators, and carbohydrate metabolisms, whereas downregulated DEGs were related to photosynthesis, response to oxidative stress, glucosinolate, and secondary metabolite biosynthesis. Our transcriptome data suggest that Cd triggers ROS production and photosynthesis decline associated with increased proteolysis through ubiquitin-proteasome system (UPS)- and chloroplast-proteases and in this way brings about re-mobilization of N and C stores into amino acids and sugars. Meanwhile, declined glucosinolate metabolism in favor of chelator synthesis and upregulation of dehydrins as inferred from transcriptome analysis confers shoots some tolerance to the HM-derived ionic/osmotic imbalances. Thus, the induction of leaf senescence might be a major long-term response of HM-sensitive plants to Cd toxicity.

Innate, High Tolerance to Zinc and Lead in Violets Confirmed at the Suspended Cell Level

Many species of the Viola L. genus (violets) colonize areas with high concentrations of trace elements in the soil, e.g., nickel, cadmium, zinc, and lead. Although tolerance to heavy metals is a common phenomenon in violets, it is not clear whether this is the result of gradual microevolutionary processes as a part of the adaptation to the specific conditions, or whether the tolerance was inherited from the ancestor(s). We developed cell suspension cultures of five plant species: two non-metallophytes-Arabidopsis thaliana (Col-0) and Viola · wittrockiana, and three metallophytes-V. philippica, V. tricolor, and Silene vulgaris subsp. humilis for tolerance tests. The aim of the study was to measure the level of tolerance of violets in comparison with species from the other genera to verify the hypothesis of the high, innate tolerance of the former. We measured cell viability, non-enzymatic antioxidant content, and the accumulation of heavy metals after cell treatment with Zn or Pb. The results indicate they are innate and independent on the ecological status (metallophyte vs. non-metallophyte) and high in comparison with other species tolerance to Zn and Pb in violets. Viability of the cells after Zn and Pb (1000 μM) exposure for 72 h was the highest in violets. Antioxidant content, after heavy metal treatment, increased significantly, particularly in metallophyte violets, indicating their high responsivity to metals. In all species, lead was detected in the protoplasm of the cells, not in the vacuole or cell wall. All violets were characterized by the accumulation capacity of lead. Here, we clearly show that the physiological and biochemical studies conducted with the use of heavy metals on plant cells translate into the heavy metal tolerance of the species.

Pieces of evidence of enhanced cellulose biosynthesis in the low-Cd cultivar and high expression level of transportation genes in the high-Cd cultivar of Lactuca sativa

To investigate the molecular mechanism of Cd-accumulating difference between Lactuca sativa cultivars, full-length transcriptome comparison, as well as biochemical validation, have been conducted between Cd pollution-safe cultivar (Cd-PSC, cv. LYDL) and high-Cd-accumulating cultivar (cv. HXDWQ). The full-length transcriptome of L. sativa cultivars was achieved for the first time. The results showed high Cd compartmentalization in the cell wall of cv. LYDL was ascribed to the enhanced cell wall biosynthesis under Cd stress, which was consistent with the high cellular debris Cd level (32.10-43.58%). The expression levels of transporter genes in cv. HXDWQ were about 1.19 to 1.21-fold higher than those in cv. LYDL, which was in accordance with the high ratio of easy migrative Cd chemical forms (68.59-81.98%), indicating the high Cd accumulation in the shoot of cv. HXDWQ was ascribed to the higher transportation capacity in cv. HXDWQ. Moreover, the Cd-induced endoplasmic reticulum (ER) stress was associated with the higher Cd detoxification and tolerance in cv. HXDWQ rather than in cv. LYDL. The study provides new insights into the Cd-induced transcriptomic difference between L. sativa cultivars and further contributes to the molecular breeding of L. sativa Cd-PSC.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Regulatory hubs and strategies for improving heavy metal tolerance in plants: Chemical messengers, omics and genetic engineering

Heavy metal (HM) accumulation in the agricultural soil and its toxicity is a major threat for plant growth and development. HMs disrupt functional integrity of the plants, induces altered phenological and physiological responses and slashes down qualitative crop yield. Chemical messengers such as phytohormones, plant growth regulators and gasotransmitters play a crucial role in regulating plant growth and development under metal toxicity in plants. Understanding the intricate network of these chemical messengers as well as interactions of genes/metabolites/proteins associated with HM toxicity in plants is necessary for deciphering insights into the regulatory circuit involved in HM tolerance. The present review describes (a) the role of chemical messengers in HM-induced toxicity mitigation, (b) possible crosstalk between phytohormones and other signaling cascades involved in plants HM tolerance and (c) the recent advancements in biotechnological interventions including genetic engineering, genome editing and omics approaches to provide a step ahead in making of improved plant against HM toxicities.

Remediation Techniques for Cadmium-Contaminated Dredged River Sediments after Land Disposal

This paper examines the remediation techniques of cadmium (Cd)-contaminated dredged river sediments after land disposal in a city in East China. Three remediation techniques, including stabilization, soil leaching, and phytoremediation, are compared by analyzing the performance of the techniques for Cd-contaminated soil remediation. The experimental results showed that the stabilization technique reduced the leaching rate of soil Cd from 33.3% to 14.3%, thus effectively reducing the biological toxicity of environmental Cd, but the total amount of Cd in soil did not decrease. Leaching soil with citric acid and oxalic acid achieved Cd removal rates of 90.1% and 92.4%, respectively. Compared with these two remediation techniques, phytoremediation was more efficient and easier to implement and had less secondary pollution, but it took more time, usually several years. In this study, these three remediation techniques were analyzed and discussed from technical, economic, and environmental safety perspectives by comprehensively considering the current status and future plans of the study site. Soil leaching was found to be the best technique for timely treatment of Cd contamination in dredged river sediments after land disposal.

A meta-analysis of transcriptomic profiles reveals molecular pathways response to cadmium stress of Gramineae

As a non-essential heavy metal, cadmium (Cd) is toxic to plants. In the last 15 years, over 70 transcriptome studies have been published to decipher the molecular response mechanism against Cd stress in different plants. To extract generalization results from transcriptomic data across different plants and obtain some hub genes that respond to Cd stress, we carried out a meta-analysis of 32 published datasets. Cluster analysis revealed that plant species played a more decisive role than the media used and exposure time in the transcriptome patterns of plant roots response to Cd. The datasets from a Gramineae-like (GL) group were closer in clustering. 838 DEGs were commonly Cd-regulated in at least nine of 18 GL datasets. Gene ontology and KEGG pathway analyses revealed that oxidative stress-related terms and lignin synthesis-related terms were significantly enriched. Mapman analysis revealed that these common DEGs were mainly involved in regulation, cellular response, secondary metabolism, transport, cell wall and lipid metabolism. In Oryza sativa, 15 DEGs were up-regulated in at least four of five HM (As, Cr, Cd, Hg and Pb) groups, such as Os10g0517500 (methionine gamma-lyase) and Os01g0159800 (bHLH107). Moreover, our datasets can be used to retrieve log2FC value of specific genes across 29 studies (48 datasets), which provides data reference for the subsequent selection of HM-related genes. Our results provide the basis for further understanding of Cd tolerance mechanisms in plants.

High salinity acclimatization alleviated cadmium toxicity in Dunaliella salina: Transcriptomic and physiological evidence

In the present study, we tested the hypothesis that high salinity acclimatization can mitigate cadmium (Cd) toxicity in the microalga Dunaliella salina. To this end, microalgal cells were subjected to high salinity (60 g/L) for 12 weeks until the growth rate remained stable between generations and were then exposed to 2.5 mg/L of Cd for 4 days. Acute Cd toxicity impaired cell growth by increasing Cd bioaccumulation and lipid peroxidation, which reduced cellular pigment, total protein, and glutathione content. It also significantly weakened photosynthetic efficiency and total antioxidant capacity. However, acclimatization to high salinity alleviated these negative effects under Cd stress. To understand the potential mechanisms behind this phenomenon, 12 cDNA libraries from control, Cd-exposed (Cd), high salinity-acclimated (Salinity), and high salinity-acclimated with Cd exposure (Salinity + Cd) cells were derived using RNA sequencing. A total of 2019, 1799, 2150 and 1256 differentially expressed genes (DEGs) were identified from sample groups Salinity / Control, Cd / Control, Salinity + Cd / Control, and Salinity + Cd / Cd, respectively. Some of these DEGs were significantly enriched in ribosome, photosynthesis, stress defense, and photosynthesis-antenna proteins. Among these genes, 82 ribosomal genes were up-regulated in Salinity / Control (corrected P = 3.8 × 10^-28), while 81 were down-regulated in Cd / Control (corrected P = 1.1 × 10^-24). Moreover, high salinity acclimatization up-regulated 8 photosynthesis genes and 18 stress defense genes compared with the control. Additionally, 3 photosynthesis genes, 11 stress defense genes and 11 genes encoding light harvesting proteins were up-regulated by high salinity acclimatization under Cd exposure. Overall, high salinity acclimatization mitigated Cd toxicity, possibly by up-regulating the transcription of photosynthesis, stress defense, and ribosomal genes. These results provide new insights on cross-tolerance in microalgae.

Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration

Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.