Genome-Wide Identification, Comprehensive Gene Feature, Evolution, and Expression Analysis of Plant Metal Tolerance Proteins in Tobacco Under Heavy Metal Toxicity

The members of zinc finger-homeodomain (ZF-HD) transcription factors are associated with abiotic stresses in soybean: insights from genomics and expression analysis

BACKGROUND

Zinc finger homeodomain (ZF-HD) belongs to the plant-specific transcription factor (TF) family and is widely involved in plant growth, development and stress responses. Despite their importance, a comprehensive identification and analysis of ZF-HD genes in the soybean (Glycine max) genome and their possible roles under abiotic stress remain unexplored.

RESULTS

In this study, 51 ZF-HD genes were identified in the soybean genome that were unevenly distributed on 17 chromosomes. All GmZF-HD genes contained a conserved ZF-HD_dimer domain and had diverse physicochemical features. Furthermore, the GmZF-HD gene structures exhibited 3 to 10 conserved motifs, and most of them showed intronless gene structures. Phylogenetic analysis categorized them into eight major groups with the highest closeness to dicots including Brassica rapa and Malus domestica. The cis-element analysis recognized plant growth and development (10%), phytohormones (31%) and stress-responsive (59%) elements. Synteny analysis identified 73 segmental and 1 tandem duplicated genes that underwent purifying selection. The collinearity analysis revealed that GmZF-HD genes showed higher homology with dicot species, indicating common ancestors with close evolutionary relationships. A total of 94 gma-miRNAs from 41 diverse miRNA families were identified, targeting 40 GmZF-HD genes, with GmZF-HD6 being most targeted by 7 miRNAs, and gma-miR4993 emerging as the dominant miRNA family. Different TFs including ERF, LBD, BBR-BPC and MYB, etc., were predicted in all 51 GmZF-HD genes upstream regions and visualized in the network. Expression profiling through RNA-Seq showed diverse expressions of GmZF-HD genes in different tissues including seeds, roots, shoots and leaves under diverse conditions. Further, the qRT-PCR analysis demonstrated that all tested GmZF-HD genes were significantly induced in soybean leaves, mainly the GmZF-HD5/6/13/39 and GmZF-HD45 genes were significantly upregulated (2.5 to 8.8 folds) under the tested stress treatments compared to control, highlighting their potential roles in response to stresses in soybean.

CONCLUSION

Overall, this study reveals comprehensive insights into the ZF-HD genes in soybeans and provides a valuable contribution towards functional studies for soybean improvement under stress conditions.

Overexpression of PagLOL1b improves drought tolerance through increasing water use efficiency and reactive oxygen species scavenging in transgenic poplar

LESION SIMULATING DISEASE1 (LSD) family genes play a key role in plant response to abiotic and biotic stress. However, their functions in the resistance of tree to drought stress are still largely not clear. Here, five LSD family genes in poplar genome were identified. Phylogenetic and collinear relationship analysis showed that they belonged to LSD, LSD-one-like 1 (LOL1) and LSD-one-like 2 (LOL2) subfamilies, and experienced two segmental duplication events. PagLSDs were highly conserved in gene structure, and all PagLSDs contained at least two LSD domains. Expression pattern and cis-acting element analyses showed that PagLSDs were widely expressed in different organs, significantly induced by polyethylene glycol, and possessed a great number of plant growth, development, plant hormones, and biotic and abiotic stress elements in their promoter regions. Further physiological experiments with transgenic poplar plants revealed that overexpression of PagLOL1b significantly enhanced the drought tolerance of transgenic plants. The improved drought tolerance was closely associated with the significant increase in stomatal closure, water use efficiency, antioxidant enzyme gene expression and antioxidant enzyme activity in transgenic plants. The results in our study imply that PagLOL1b has great potential in the engineering of new tree varieties resistant to drought stress.

Genome-wide identification of metal tolerance protein genes in Quercus dentata and their roles in response to various heavy metal stresses

Metal tolerance protein (MTP) is a cation transporter that plays an important role in tolerance to heavy metal stress. However, thus far, there has been no genome-wide investigation of the MTP gene family in Quercus plants. Quercus dentata is one of the main constructive species of forest in northern China. It has strong tolerance to a variety of heavy metal stresses. In this study, 25 MTPs were identified from the Q. dentata genome and classified into three subfamilies and seven groups according to their sequence characteristics and phylogenetic relationships. Both tandem and segmental duplication events contributed to the expansion of the QdMTP gene family. Interestingly, all 10 tandem duplication events contributed to the expansion of the Mn-CDF subfamily. The expression of Mn-CDF subfamily members in different organs and tissues of Q. dentata was different, and they responded differently to manganese, iron, zinc and cadmium stress treatments. QdMTP10.7, a member of the Mn-CDF subfamily, enhanced yeast growth under manganese, zinc and iron stresses. The subcellular localization in tobacco leaf epidermis cells showed that QdMTP10.7 was located in vacuoles. These data generated from this study provide an important foundation to elucidate the biological roles of QdMTP genes related to heavy metal tolerance in Q. dentata.

Characterization of a Nicotiana tabacum phytochelatin synthase 1 and its response to cadmium stress

Phytochelatin synthase (PCS) is a critical enzyme involved in heavy metal detoxification in organisms. In this study, we aim to comprehensively investigate the molecular and functional characteristics of the PCS1 gene from Nicotiana tabacum by examining its enzymatic activity, tissue-specific expression pattern, Cd-induced expression, as well as the impact on Cd tolerance and accumulation. The results demonstrated that the amino acid sequence of NtPCS1 shared a high similarity in its N-terminal region with PCS from other species. The enzymatic activity of NtPCS1 was found to be enhanced in the order Ag2+ > Cd2+ > Cu2+ > Pb2+ > Hg2+ > Fe2+ > Zn2+. In addition, RT-PCR data indicated that NtPCS1 gene is constitutively expressed, with the highest expression observed in flowers, and that its transcript levels are up-regulated by CdCl2. When tobacco overexpressing NtPCS1 (PCS1 lines) were grown under CdCl2 stress, they produced more phytochelatins (PCs) than WT plants, but this did not result in increased Cd accumulation. However, in a root growth assay, the PCS1 lines exhibited hypersensitivity to Cd. The overexpression of NtPCS1 itself does not appear to be the primary cause of this heightened sensitivity to Cd, as the Arabidopsis thaliana Atpcs1 mutant overexpressing NtPCS1 actually exhibited enhanced tolerance to Cd. Furthermore, the addition of exogenous glutathione (GSH) progressively reduced the Cd hypersensitivity of the PCS1 lines, with the hypersensitivity even being completely eliminated. Surprisingly, the application of exogenous GSH led to a remarkably enhanced Cd accumulation in the PCS1 lines. This study enriches our understanding of the molecular function of the NtPCS1 gene and suggests a promising avenue for Cd tolerance through the heterologous expression of PCS genes in different species.

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

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

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

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

Genome-wide identification, expression and function analysis of the MTP gene family in tulip (Tulipa gesneriana)

Currently, soil heavy metal contamination is a severe issue, particularly with Cd pollution. The metal tolerance protein (MTP) proteins, as plant divalent cation transporters, play a crucial role in the transport and tolerance of heavy metals in plants. This study conducted comprehensive identification and characterization of the MTP gene family in the tulip. A total of 11 TgMTP genes were identified and phylogenetically classified into three subfamilies. Conserved motif and gene structure analyses unveiled commonalities and variations among subfamily members. Expression profiling demonstrated several TgMTPs were markedly upregulated under Cd exposure, including the TgMTP7.1. Heterologous expression in yeast validated that TgMTP7.1 could ameliorate Cd sensitivity and enhance its tolerance. These results provide primary insights into the MTP gene family in tulip. Phylogenetic relationships and functional analyses establish a framework for elucidating the transporters and molecular mechanisms governing Cd accumulation and distribution in tulip. Key TgMTPs identified, exemplified by TgMTP7.1, may illuminate molecular breeding efforts aimed at developing Cd-tolerant cultivars for the remediation of soil Cd contamination.

Genome-Wide Identification and Expression Analysis of MTP (Metal Ion Transport Proteins) Genes in the Common Bean

MTP/CDF carriers, called metal ion transport proteins, act as substrates for the transmission of micronutrients such as iron (Fe), zinc (Zn), and manganese (Mn) to membrane carriers in plants. In this study, genome-wide analysis of the MTP gene family in the common bean genome, expression analysis of the PvMTP4, PvMTP5, and PvMTP12 genes after Fe and Zn treatments, and the effects of Fe and Zn applications on iron and zinc content were investigated. This study used common bean genotypes assumed to have high or low Fe and Zn accumulation ability. PvMTP genes were defined as containing conserved catalytic domains with molecular weights and protein lengths ranging from 41.35 to 91.05 kDa and from 369 to 813 amino acids (aa), respectively. As a result of the phylogenetic analysis, three main clusters containing seven subgroups were formed. In this study, the first characterization of the MTP gene family of beans was performed, and the responses of three different PvMTP genes in the Zn-CDF group to Fe and Zn applications were revealed. The obtained findings are thought to constitute pioneering resources for future research on common bean biofortification studies, plant breeding related to Fe and Zn, and the functional characterization of the MTP gene family.

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

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

Deciphering the functional roles of transporter proteins in subcellular metal transportation of plants

MAIN CONCLUSION

The role of transporters in subcellular metal transport is of great significance for plants in coping with heavy metal stress and maintaining their proper growth and development. Heavy metal toxicity is a serious long-term threat to plant growth and agricultural production, becoming a global environmental concern. Excessive heavy metal accumulation not only damages the biochemical and physiological functions of plants but also causes chronic health hazard to human beings through the food chain. To deal with heavy metal stress, plants have evolved a series of elaborate mechanisms, especially a variety of spatially distributed transporters, to strictly regulate heavy metal uptake and distribution. Deciphering the subcellular role of transporter proteins in controlling metal absorption, transport and separation is of great significance for understanding how plants cope with heavy metal stress and improving their adaptability to environmental changes. Hence, we herein introduce the detrimental effects of excessive common essential and non-essential heavy metals on plant growth, and describe the structural and functional characteristics of transporter family members, with a particular emphasis on their roles in maintaining heavy metal homeostasis in various organelles. Besides, we discuss the potential of controlling transporter gene expression by transgenic approaches in response to heavy metal stress. This review will be valuable to researchers and breeders for enhancing plant tolerance to heavy metal contamination.

Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses

Metal tolerance proteins (MTPs) as Me²⁺/H⁺(K⁺) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd²⁺ and Cu²⁺ exposure might be responsible for metal translocation from roots to leaves.

Tobacco as an efficient metal accumulator

Tobacco (Nicotiana tabacum L.) is an important industrial crop plant. However, it efficiently accumulates metals, primarily cadmium (Cd) and also zinc (Zn), in its leaves. Therefore, it could be a source of cadmium intake by smokers. On the other hand, as a high leaf metal accumulator, it is widely used for phytoremediation of metal-contaminated soil. Both issues provide an important rationale for investigating the processes regulating metal homeostasis in tobacco. This work summarizes the results of research to date on the understanding of the molecular mechanisms determining the effective uptake of Zn and Cd, their translocation into shoots and accumulation in leaves. It also discusses the current state of research to improve the phytoremediation properties of tobacco through genetic modification and to limit leaf Cd content for the tobacco industry.

Genome-wide identification and expression analysis of metal tolerance protein (MTP) gene family in soybean (Glycine max) under heavy metal stress

AIM

Plant metal tolerance proteins (MTPs) are plant membrane divalent cation transporters that specifically contribute to heavy metal stress resistance and mineral uptake. However, little is known about this family's molecular behaviors and biological activities in soybean.

METHODS AND RESULTS

A total of 20 potential MTP candidate genes were identified and studied in the soybean genome for phylogenetic relationships, chromosomal distributions, gene structures, gene ontology, cis-elements, and previous gene expression. Furthermore, the expression of MTPs has been investigated under different heavy metals treatments. All identified soybean MTPs (GmaMTPs) contain a cation efflux domain or a ZT dimer and are further divided into three primary cation diffusion facilitator (CDF) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The developmental analysis reveals that segmental duplication contributes to the GmaMTP family's expansion. Tissue-specific expression profiling revealed comparative expression profiling in similar groups, although gene expression differed between groups. GmaMTP genes displayed biased responses in either plant leaves or roots when treated with heavy metal. In the leaves and roots, nine and ten GmaMTPs responded to at least one metal ion treatment. Furthermore, in most heavy metal treatments, GmaMTP1.1, GmaMTP1.2, GmaMTP3.1, GmaMTP3.2, GmaMTP4.1, and GmaMTP4.3 exhibited significant expression responses.

CONCLUSION

Our findings provided insight into the evolution of MTPs in soybean. Overall, our findings shed light on the evolution of the MTP gene family in soybean and pave the path for further functional characterization of this gene family.

Metal tolerance gene family in barley: an in silico comprehensive analysis

Metal-tolerance proteins (MTPs) are divalent cation transporters that play critical roles in metal tolerance and ion homeostasis in plants. However, a comprehensive study of MTPs is still lacking in crop plants. The current study aimed to comprehensively identify and characterize the MTP gene family in barley (Hordeum vulgare, Hv), an important crop. In total, 12 HvMTPs were identified in the barley genome in this study. They were divided into three phylogenetic groups (Zn-cation diffusion facilitator proteins [CDFs], Fe/Zn-CDFs, and Mn-CDFs) and further subdivided into seven groups (G1, G5, G6, G7, G8, G9, and G12). The majority of MTPs were hydrophobic proteins found in the vacuolar membrane. Gene duplication analysis of HvMTPs revealed one pair of segmental-like duplications in the barley genome. Evolutionary analysis suggested that barley MTPs underwent purifying natural selection. Additionally, the HvMTPs were analyzed in the pan-genome sequences of barley (20 accessions), which suggests that HvMTPs are highly conserved in barley evolution. Cis-acting regulatory elements, microRNA target sites, and protein-protein interaction analysis indicated the role of HvMTPs in a variety of biological processes. Expression profiling suggests that HvMTPs play an active role in maintaining barley nutrient homeostasis throughout its life cycle, and their expression levels were not significantly altered by abiotic stresses like cold, drought, or heat. The expression of barley HvMTP genes in the presence of heavy metals such as Zn²⁺, Cu²⁺, As³⁺, and Cd²⁺ revealed that these MTPs were induced by at least one metal ion, implying their involvement in metal tolerance or transportation. The identification and comprehensive investigation of MTP gene family members will provide important gene resources for the genetic improvement of crops for metal tolerance, bioremediation, or biofortification of staple crops.

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

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

Genome-Wide Identification and Expressional Profiling of the Metal Tolerance Protein Gene Family in Brassica napus

The Cation Diffusion Facilitator (CDF) family, also named Metal Tolerance Protein (MTP), is one of the gene families involved in heavy metal transport in plants. However, a comprehensive study of MTPs in Brassica napus has not been reported yet. In the present study, we identified 33 BnMTP genes from the rapeseed genome using bioinformatic analyses. Subsequently, we analyzed the phylogenetic relationship, gene structure, chromosome distribution, conserved domains, and motifs of the BnMTP gene family. The 33 BnMTPs were phylogenetically divided into three major clusters (Zn-CDFs, Fe/Zn-CDFs, and Mn-CDFs) and seven groups (group 1, 5, 6, 7, 8, 9, and 12). The structural characteristics of the BnMTP members were similar in the same group, but different among groups. Evolutionary analysis indicated that the BnMTP gene family mainly expanded through whole-genome duplication (WGD) and segmental duplication events. Moreover, the prediction of cis-acting elements and microRNA target sites suggested that BnMTPs might be involved in plant growth, development, and stress responses. In addition, we found the expression of 24 BnMTPs in rapeseed leaves or roots could respond to heavy metal ion treatments. These results provided an important basis for clarifying the biological functions of BnMTPs, especially in heavy metal detoxification, and will be helpful in the phytoremediation of heavy metal pollution in soil.

Genome-wide Identification of Metal Tolerance Protein Genes in Peanut: Differential Expression in the Root of Two Contrasting Cultivars Under Metal Stresses

Metal tolerance proteins (MTP) are Me²⁺/H⁺(K⁺) antiporters that play important roles in the transport of divalent cations in plants. However, their functions in peanut are unknown. In the present study, a total of 24 AhMTP genes were identified in peanut, which were divided into seven groups belonging to three substrate-specific clusters (Zn-CDFs, Zn/Fe-CDFs, and Mn-CDFs). All AhMTP genes underwent whole genome or segmental gene duplication events except AhMTP12. Most AhMTP members within the same subfamily or group generally have similar gene and protein structural characteristics. However, some genes, such as AhMTP1.3, AhMTP2.4, and AhMTP12, showed wide divergences. Most of AhMTP genes preferentially expressed in reproductive tissues, suggesting that these genes might play roles in metal transport during the pod and seed development stages. Excess metal exposure induced expressions for most of AhMTP genes in peanut roots depending on cultivars. By contrast, AhMTP genes in the root of Fenghua 1 were more sensitive to excess Fe, Cd, and Zn exposure than that of Silihong. Stepwise linear regression analysis showed that the percentage of Fe in shoots significantly and positively correlated with the expression of AhMTP4.1, AhMTP9.1, and AhMTPC4.1, but negatively correlated with that of AhMTPC2.1 and AhMTP12. The expression of AhMTP1.1 showed a significant and negative correlation with the percentage of Mn in shoots. The percentage of Zn in shoots was significantly and positively correlated with the expression of AhMTP2.1 but was negatively correlated with that of AhMTPC2.1. The differential responses of AhMTP genes to metal exposure might be, at least partially, responsible for the different metal translocation from roots to shoots between Fenghua 1 and Silihong.

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

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

Comprehensive genome wide identification and expression analysis of MTP gene family in tomato (Solanum lycopersicum) under multiple heavy metal stress

Plant metal tolerance proteins (MTPs) play major roles in enhancing resistance to heavy metal tolerance and homeostasis. However, the role of MTPs genes in tomato, which is one of the most popular crops, is still largely limited. Hence, we investigated genome-wide study of tomato MTPs, including phylogenetic, duplication, gene structure, gene ontology and previous transcriptomic data analysis. Moreover, the MTPs expression behaviour under various heavy metals stress has rarely been investigated. In the current study, eleven MTP candidate genes were genome-wide identified and classified into three major groups; Mn-cation diffusion facilitators (CDFs), Fe/Zn-CDFs, and Zn-CDFs based on the phylogeny. Structural analysis of SlMTPs showed high gene similarity within the same group with cation_efflux or ZT_dimerdomains. Evolutionary analysis revealed that segmental duplication contributed to the expansion of the SlMTP family. Gene ontology further showed the vital roles of MTPs in metal-related processes. Tissue-specific expression profiling exhibited similar expression patterns in the same group, whereas gene expression varied among groups. The MTPs expression was evaluated after tomato treatments by five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). SlMTP genes displayed differential responses in either plant leaves or roots under heavy metals treatments. Nine and ten SlMTPs responded to at least one metal ion treatment in leaves and roots, respectively. In addition SlMTP1, SlMTP3, SlMTP4, SlMTP8, SlMTP10 and SlMTP11 exhibited the highest expression responses in most of heavy metals treatments. Overall, our findings presented a standpoint on the evolution of MTPs and their evolution in tomato and paved the way for additional functional characterization under heavy metal toxicity.

Characterization of Metal Tolerance Proteins and Functional Analysis of GmMTP8.1 Involved in Manganese Tolerance in Soybean

Manganese is an essential micronutrient for plant growth but can be toxic to plants when it reaches excessive levels. Although metal tolerance proteins (MTPs), which belong to the cation diffusion facilitator (CDF) family, have been demonstrated to play critical roles in manganese (Mn) tolerance in plants, the characteristics and functions of GmMTP members in the response of soybean (Glycine max) to Mn toxicity have not been documented. In this study, growth inhibition was observed in soybean plants that were exposed to a toxic level of Mn in hydroponics, as reflected by the generation of brown spots, and decreased leaf chlorophyll concentration and plant fresh weight. Subsequent genome-wide analysis resulted in the identification of a total of 14 GmMTP genes in the soybean genome. Among these GmMTPs, 9 and 12 were found to be regulated by excess Mn in leaves and roots, respectively. Furthermore, the function of GmMTP8.1, a Mn-CDF homologue of ShMTP8 identified in the legume Stylosanthes hamata that is involved in Mn detoxification, was characterized. Subcellular localization analysis showed that GmMTP8.1 was localized to the endoplasmic reticulum (ER). Heterologous expression of GmMTP8.1 led to the restoration of growth of the Mn-hypersensitive yeast (Saccharomyces cerevisiae) mutant Δpmr1, which is made defective in Mn transport into the Golgi apparatus by P-type Ca/Mn-ATPase. Furthermore, GmMTP8.1 overexpression conferred tolerance to the toxic level of Mn in Arabidopsis (Arabidopsis thaliana). Under excess Mn conditions, concentrations of Mn in shoots but not roots were decreased in transgenic Arabidopsis, overexpressing GmMTP8.1 compared to the wild type. The overexpression of GmMTP8.1 also led to the upregulation of several transporter genes responsible for Mn efflux and sequestration in Arabidopsis, such as AtMTP8/11. Taken together, these results suggest that GmMTP8.1 is an ER-localized Mn transporter contributing to confer Mn tolerance by stimulating the export of Mn out of leaf cells and increasing the sequestration of Mn into intracellular compartments.

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress

Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd²⁺, Co²⁺, Mn²⁺, Zn²⁺, and Fe²⁺). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.

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

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

Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population?

Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth's system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21-34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, "quantum-leap" improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a "quantum-leap" include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.

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.

Genome-Wide Identification, Structure Characterization, Expression Pattern Profiling, and Substrate Specificity of the Metal Tolerance Protein Family in Canavalia rosea (Sw.) DC

Plant metal tolerance proteins (MTPs) play key roles in heavy metal absorption and homeostasis in plants. By using genome-wide and phylogenetic approaches, the origin and diversification of MTPs from Canavalia rosea (Sw.) DC. was explored. Canavalia rosea (bay bean) is an extremophile halophyte with strong adaptability to seawater and drought and thereby shows specific metal tolerance with a potential phytoremediation ability. However, MTP genes in leguminous plants remain poorly understood. In our study, a total of 12 MTP genes were identified in C. rosea. Multiple sequence alignments showed that all CrMTP proteins possessed the conserved transmembrane domains (TM1 to TM6) and could be classified into three subfamilies: Zn-CDFs (five members), Fe/Zn-CDFs (five members), and Mn-CDFs (two members). Promoter cis-acting element analyses revealed that a distinct number and composition of heavy metal regulated elements and other stress-responsive elements existed in different promoter regions of CrMTPs. Analysis of transcriptome data revealed organ-specific expression of CrMTP genes and the involvement of this family in heavy metal stress responses and adaptation of C. rosea to extreme coral reef environments. Furthermore, the metal-specific activity of several functionally unknown CrMTPs was investigated in yeast. These results will contribute to uncovering the potential functions and molecular mechanisms of heavy metal absorption, translocation, and accumulation in C. rosea plants.

Tonoplast-associated calcium signaling regulates manganese homeostasis in Arabidopsis

Manganese (Mn) is an essential micronutrient in plants. However, excessive Mn absorption in acidic and waterlogged soils can lead to Mn toxicity. Despite their essential roles in Mn homeostasis, transcriptional and post-transcriptional modifications of Mn transporters remain poorly understood. Here, we demonstrated that high-Mn stress induces an obvious Ca²⁺ signature in Arabidopsis. We identified four calcium-dependent protein kinases, CPK4/5/6/11, that interact with the tonoplast-localized Mn and iron (Fe) transporter MTP8 in vitro and in vivo. The cpk4/5/6/11 quadruple mutant displayed a dramatic high-Mn-sensitive phenotype similar to that of the mtp8 mutant. CPKs phosphorylated the N-terminal domain of MTP8 primarily at the Ser31 and Ser32 residues. Transport assays combined with multiple physiological experiments on phospho-dead variant MTP8^S31/32A and phospho-mimetic variant MTP8^S31/32D plants under different Mn and Fe conditions suggested that Ser31 and Ser32 are crucial for MTP8 function. In addition, genetic analysis showed that CPKs functioned upstream of MTP8. In summary, we identified a tonoplast-associated calcium signaling cascade that orchestrates Mn homeostasis and links Mn toxicity, Ca²⁺ signaling, and Mn transporters. These findings provide new insight into Mn homeostasis mechanisms and Ca²⁺ signaling pathways in plants, providing potential targets for engineering heavy metal toxicity-tolerant plants.

Identification and characterization of a tobacco metal tolerance protein, NtMTP2

Metal tolerance proteins (MTPs) from the CDF (Cation Diffusion Facilitator) family are efflux transporters that play a crucial role in metal homeostasis by maintaining optimal metal concentrations in the cytoplasm. Here, a novel tobacco NtMTP2 transporter was cloned and characterized. It encodes a 512 aa protein containing all specific CDF family domains. A GFP-NtMTP2 fusion protein localizes to the tonoplast in tobacco cells. NtMTP2 expression in yeast conferred tolerance to Co and Ni, indicating that the protein mediates transport of both metals, but not Zn, Mn, Cu, Fe, or Cd. Nonetheless, the expression level was not affected by Co or Ni, except for an increase in leaves at high Co concentrations. Its expression in plant parts remained stable during development, but increased in the leaves of older plants. Analysis of tobacco expressing a promoter-GUS construct indicates that the main sites of promoter activity are the conductive tissue throughout the plant and the palisade parenchyma in leaves. Our results suggest that NtMTP2 is a tonoplast transporter mediating sequestration of Co and Ni into vacuoles and an important housekeeping protein that controls the basal availability of micronutrients and plays a role in the sequestration of metal excess, specifically in leaves.

Heavy Metal Transporters-Associated Proteins in S. tuberosum: Genome-Wide Identification, Comprehensive Gene Feature, Evolution and Expression Analysis

Plants have evolved a number of defense and adaptation responses to protect themselves against challenging environmental stresses. Genes containing a heavy metal associated (HMA) domain are required for the spatiotemporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by StHMA genes, we identified 36 gene members in the StHMA family and divided them into six subfamilies by phylogenetic analysis. The StHMAs had high collinearity and were segmentally duplicated. Structurally, most StHMAs had one HMA domain, StHIPPc and StRNA1 subfamilies had two, and 13 StHMAs may be genetically variable. The StHMA gene structures and motifs varied considerably among the various classifications, this suggests the StHMA family is diverse in genetic functions. The promoter analysis showed that the StHMAs had six main cis-acting elements with abiotic stress. An expression pattern analysis revealed that the StHMAs were expressed tissue specifically, and a variety of abiotic stresses may induce the expression of StHMA family genes. The HMA transporter family may be regulated and expressed by a series of complex signal networks under abiotic stress. The results of this study may help to establish a theoretical foundation for further research investigating the functions of HMA genes in Solanum tuberosum to elucidate their regulatory role in the mechanism governing the response of plants to abiotic stress.

Heavy Metal Stress-Associated Proteins in Rice and Arabidopsis: Genome-Wide Identification, Phylogenetics, Duplication, and Expression Profiles Analysis

Heavy metal exposure is a serious environmental stress in plants. However, plants have evolved several strategies to improve their heavy metal tolerance. Heavy metal-associated proteins (HMPs) participate in heavy metal detoxification. Here, we identified 46 and 55 HMPs in rice and Arabidopsis, respectively, and named them OsHMP 1–46 and AtHMP 1–55 according to their chromosomal locations. The HMPs from both plants were divided into six clades based on the characteristics of their heavy metal-associated domains (HMA). The HMP gene structures and motifs varied greatly among the different classifications. The HMPs had high collinearity and were segmentally duplicated. A cis-element analysis revealed that the HMPs may be regulated by different transcription factors. An expression profile analysis disclosed that only eight OsHMPs were constitutive in rice tissues. Of these, the expression of OsHMP37 was far higher than that of the other seven genes while OsHMP28 was expressed exclusively in the roots. For Arabidopsis, nine AtHMPs presented with very high transcript levels in all organs. Most of the selected OsHMPs were differentially expressed in various tissues under different heavy metal stresses. Only OsHMP09, OsHMP18, and OsHMP22 showed higher expression levels in all tissues under different heavy metal stresses. In contrast, most of the selected AtHMPs had nearly constant expression levels in different tissues under various heavy metal stresses. The AtHMP20, AtHMP23, AtHMP25, AtHMP31, AtHMP35, AtHMP46 expression levels under different heavy metal stresses were higher in the leaves and roots. The foregoing discoveries elucidated HMP evolution in monocotyledonous and dicotyledonous plants and may helpful functionally characterize HMPs in the future.

Manganese in Plants: From Acquisition to Subcellular Allocation

Manganese (Mn) is an important micronutrient for plant growth and development and sustains metabolic roles within different plant cell compartments. The metal is an essential cofactor for the oxygen-evolving complex (OEC) of the photosynthetic machinery, catalyzing the water-splitting reaction in photosystem II (PSII). Despite the importance of Mn for photosynthesis and other processes, the physiological relevance of Mn uptake and compartmentation in plants has been underrated. The subcellular Mn homeostasis to maintain compartmented Mn-dependent metabolic processes like glycosylation, ROS scavenging, and photosynthesis is mediated by a multitude of transport proteins from diverse gene families. However, Mn homeostasis may be disturbed under suboptimal or excessive Mn availability. Mn deficiency is a serious, widespread plant nutritional disorder in dry, well-aerated and calcareous soils, as well as in soils containing high amounts of organic matter, where bio-availability of Mn can decrease far below the level that is required for normal plant growth. By contrast, Mn toxicity occurs on poorly drained and acidic soils in which high amounts of Mn are rendered available. Consequently, plants have evolved mechanisms to tightly regulate Mn uptake, trafficking, and storage. This review provides a comprehensive overview, with a focus on recent advances, on the multiple functions of transporters involved in Mn homeostasis, as well as their regulatory mechanisms in the plant's response to different conditions of Mn availability.

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

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

Molecular characterization and expression dynamics of MTP genes under various spatio-temporal stages and metal stress conditions in rice

Metal Tolerance Proteins (MTPs) are the class of membrane proteins involved in the transport of metals, mainly Zn, Mn, Fe, Cd, Co and Ni, and confer metal tolerance in plants. In the present study, a comprehensive molecular analysis of rice MTP genes was performed to understand the evolution, distribution and expression dynamics of MTP genes. Exploration of the whole genome re-sequencing information available for three thousand rice genotypes highlighted the evolution and allelic diversity of MTP genes. Based on the presence of non-synonymous single nucleotide polymorphism (SNP), MTP1, MTP6, MTP8 and MTP9 were found to be the most conserved genes. Furthermore, results showed localization of MTP1, MTP8.1 and MTP9, and MTP11, respectively with QTLs/m-QTLs for Zn and Cd accumulation, making these genes promising candidates to understand the QTL regulation. Expression profiling of the entire set of 10 MTP genes revealed root and shoot specific expressions of MTP9 and MTP8.1, respectively, under all tested vegetative stages. Expression of seed-specific MTPs increased as seed maturation progressed, which revealed their potential role in transporting metals during seed filling. Upon exposure to harmful heavy metals, expression of most MTP genes decreased in root and increased in shoot, suggests that different mechanisms are being employed by MTPs in different tissues. Contrastingly, only a few MTPs were found to be responsive to Fe and/or Zn starvation conditions. The extensive analysis of MTPs presented here will be helpful in identifying candidate MTP genes for crop biofortification and bioremediation purposes.