Comparative expression analysis of heavy metal ATPase subfamily genes between Cd-tolerant and Cd-sensitive turnip landraces

Genome-wide identification of heavy-metal ATPases genes in Areca catechu: investigating their functionality under heavy metal exposure

Heavy-metal ATPases (HMAs) play a vital role in plants, helping to transport heavy metal ions across cell membranes.However, insufficient data exists concerning HMAs genes within the Arecaceae family.In this study, 12 AcHMA genes were identified within the genome of Areca catechu, grouped into two main clusters based on their phylogenetic relationships.Genomic distribution analysis reveals that the AcHMA genes were unevenly distributed across six chromosomes. We further analyzed their physicochemical properties, collinearity, and gene structure.Furthermore, RNA-seq data analysis exhibited varied expressions in different tissues of A. catechu and found that AcHMA1, AcHMA2, and AcHMA7 were highly expressed in roots, leaves, pericarp, and male/female flowers. A total of six AcHMA candidate genes were selected based on gene expression patterns, and their expression in the roots and leaves was determined using RT-qPCR under heavy metal stress. Results showed that the expression levels of AcHMA1 and AcHMA3 genes were significantly up-regulated under Cd2 + and Zn2 + stress. Similarly, in response to Cu2+, the AcHMA5 and AcHMA8 revealed the highest expression in roots and leaves, respectively. In conclusion, this study will offer a foundation for exploring the role of the HMAs gene family in dealing with heavy metal stress conditions in A. catechu.

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

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

Ionomic analysis reveals the mechanism of mercaptosilane-modified palygorskite on reducing Cd transport from soil to wheat

Mercaptosilane-modified palygorskite (MP) can immobilize Cd in acid soil and reduce the enrichment of Cd in rice. However, the immobilization effect and its durability on alkaline field were unclear. Meanwhile, whether MP could reduce Cd in different wheat parts at different stages also needs further exploration. Here, we determined the dynamic change of Cd in soil and wheat at different periods, studied the interaction mechanism at key organs, and calculated the contribution of coexisting metals on the reduction of Cd to study the effect of MP on the transfer of Cd in soil-wheat system. Results showed MP was highly effective to immobilize Cd in alkaline farmland and could take effect during the whole growing season but not change pH values. DTPA-Cd and EXE-Cd of soil were reduced by 34.88-49.71% and 49.36-84.81%, respectively, while OX-Cd was increased by 34.61-43.60% at the whole stages. Cd in grains at maturity stage was reduced from 0.118 to 0.069 mg/kg, lower than the limit standard of the China and Codex Alimentarius Commission (0.1 mg/kg). Root and nodes were critical organs influenced by MP to reduce Cd in grains, and the reduction efficiency on wheat was relatively weak at flowering and filling stage. MP regulated the antagonism or synergy effects of coexisting elements on Cd to modulate the Cd accumulation in grains. Besides, the contributions of different elements on Cd were also evaluated by path models. This will provide an important basis for the precision remediation of Cd-polluted alkaline wheat fields.

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 analysis of heavy metal ATPases (HMAs) in Poaceae species and their potential role against copper stress in Triticum aestivum

Plants require copper for normal growth and development and have evolved an efficient system for copper management based on transport proteins such as P_1B-ATPases, also known as heavy metal ATPases (HMAs). Here, we report HMAs in eleven different Poaceae species, including wheat. Furthermore, the possible role of wheat HMAs in copper stress was investigated. BlastP searches identified 27 HMAs in wheat, and phylogenetic analysis based on the Maximum Likelihood method demonstrated a separation into four distinct clades. Conserved motif analysis, domain identification, gene structure, and transmembrane helices number were also identified for wheat HMAs using computational tools. Wheat seedlings grown hydroponically were subjected to elevated copper and demonstrated toxicity symptoms with effects on fresh weight and changes in expression of selected HMAs TaHMA7, TaHMA8, and TaHMA9 were upregulated in response to elevated copper, suggesting a role in wheat copper homeostasis. Further investigations on these heavy metal pumps can provide insight into strategies for enhancing crop heavy metal tolerance in the face of heavy metal pollution.

The Effect of Cadmium on Plants in Terms of the Response of Gene Expression Level and Activity

Cadmium (Cd) is a heavy metal that can cause damage to living organisms at different levels. Even at low concentrations, Cd can be toxic to plants, causing harm at multiple levels. As they are unable to move away from areas contaminated by Cd, plants have developed various defence mechanisms to protect themselves. Hyperaccumulators, which can accumulate and detoxify heavy metals more efficiently, are highly valued by scientists studying plant accumulation and detoxification mechanisms, as they provide a promising source of genes for developing plants suitable for phytoremediation techniques. So far, several genes have been identified as being upregulated when plants are exposed to Cd. These genes include genes encoding transcription factors such as iron-regulated transporter-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) gene family, genes encoding phytochelatin synthases (PCs), superoxide dismutase (SOD) genes, heavy metal ATPase (HMA), cation diffusion facilitator gene family (CDF), Cd resistance gene family (PCR), ATP-binding cassette transporter gene family (ABC), the precursor 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and precursor 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) multigene family are also influenced. Thanks to advances in omics sciences and transcriptome analysis, we are gaining more insights into the genes involved in Cd stress response. Recent studies have also shown that Cd can affect the expression of genes related to antioxidant enzymes, hormonal pathways, and energy metabolism.

Genome-wide survey of HMA gene family and its characterization in wheat (Triticum aestivum)

Background

Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in Arabidopsis and other plants, it has not been thoroughly studied in wheat (Triticum aestivum). This study was proposed to investigate the HMA gene family in wheat.

Methods

To analyze the phylogenetic relationships, gene structure, gene ontology, and conserved motifs, a comparative study of wheat HMA genes with the Arabidopsis genome was performed.

Results

A total of 27 T. aestivum proteins belonging to the HMA gene family were identified in this study, with amino acid counts ranging from 262 to 1,071. HMA proteins were found to be grouped into three subgroups in a phylogenetic tree, and closely related proteins in the tree showed the same expression patterns as motifs found in distinct subgroups. Gene structural study elucidated that intron and exon arrangement differed by family.

Conclusion

As a result, the current work offered important information regarding HMA family genes in the T. aestivum genome, which will be valuable in understanding their putative functions in other wheat species.

Genome-wide identification and transcriptome analysis of the heavy metal-associated (HMA) gene family in Tartary buckwheat and their regulatory roles under cadmium stress

Heavy metal-associated (HMA) genes are those related to heavy metal transport and detoxification in plants. HMA genes have not been reported in Tartary buckwheat so far. In this study, we accessed the HMA genes of Tartary buckwheat by genome-wide identification for the first time. A total of 56 HMA genes were identified, including 36 ATX1 (antioxidant protein1) genes, 13 HIPP (heavy metal-associated isoprenylated plant protein) genes, and 7 P_1B-ATPase (P_1B-type adenosine triphosphatase) genes. These gene structures, motif compositions, chromosomal distribution, phylogenetic relationship, duplication events, interaction networks, cis-acting elements, and transcriptional expression under cadmium (Cd) stress were investigated. Among them, genes in HIPP and ATX1 subfamilies were more closely related. The 56 HMA genes were involved in the regulation of metal ion transport and homeostasis by binding metal ions, likely triggered by signals transducted by plant hormones. Fifteen of these HMA genes played regulatory roles under Cd stress. FtP1bA1 was identified to be a core gene involved in the defense regulation of Cd stress. Our results provide not only the first overview and characteristics of HMA genes in the whole genome of Tartary buckwheat but also a valuable reference for the functional analysis of HMA genes under Cd stress. Understanding changes in gene regulation induced by Cd stress lays the foundation for breeding resistant varieties.

Genome-wide identification and expression analysis of the JAZ gene family in turnip

JAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

Genome-wide identification and function analysis of HMAD gene family in cotton (Gossypium spp.)

BACKGROUND

The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium.

RESULTS

A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress.

CONCLUSIONS

Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.

Cadmium isotope fractionation reveals genetic variation in Cd uptake and translocation by Theobroma cacao and role of natural resistance-associated macrophage protein 5 and heavy metal ATPase-family transporters

In response to new European Union regulations, studies are underway to mitigate accumulation of toxic cadmium (Cd) in cacao (Theobroma cacao, Tc). This study advances such research with Cd isotope analyses of 19 genetically diverse cacao clones and yeast transformed to express cacao natural resistance-associated macrophage protein (NRAMP5) and heavy metal ATPases (HMAs). The plants were enriched in light Cd isotopes relative to the hydroponic solution with Δ114/110Cdtot-sol = -0.22 ± 0.08‰. Leaves show a systematic enrichment of isotopically heavy Cd relative to total plants, in accord with closed-system isotope fractionation of Δ114/110Cdseq-mob = -0.13‰, by sequestering isotopically light Cd in roots/stems and mobilisation of remaining Cd to leaves. The findings demonstrate that (i) transfer of Cd between roots and leaves is primarily unidirectional; (ii) different clones utilise similar pathways for Cd sequestration, which differ from those of other studied plants; (iii) clones differ in their efficiency of Cd sequestration. Transgenic yeast that expresses TcNRAMP5 (T. cacao natural resistance-associated macrophage gene) had isotopically lighter Cd than did cacao. This suggests that NRAMP5 transporters constitute an important pathway for uptake of Cd by cacao. Cd isotope signatures of transgenic yeast expressing HMA-family proteins suggest that they may contribute to Cd sequestration. The data are the first to record isotope fractionation induced by transporter proteins in vivo.