Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice

Evolutionarily conserved BON1 regulates the basal cytosolic Ca2+ level by calmodulin-independent activation of Ca2+ pumps in Arabidopsis

Plasma membrane-localized autoinhibited Ca2+ pumps are essential for maintaining basal cytosolic Ca2+ levels for regulating growth processes and environmental responses. These pumps are known to be activated by calmodulins to maintain Ca2+ homeostasis in plants and animals. Here, we demonstrate that the evolutionarily conserved copine protein BON1 is critical for maintaining low cytosolic Ca2+ concentrations by directly regulating two plasma membrane-localized Ca2+ pumps ACA8 and ACA10 in Arabidopsis. BON1 interacts with a region within the N-terminal domain of ACA8 and ACA10, preceding the calmodulin binding sites, and stimulates ACA8 activity. This activation can occur without calmodulin binding, indicating that BON1 and calmodulin independently regulate the Ca2+ pump. Loss of BON1 function results in elevated basal cytosolic Ca2+ concentrations, which can be partially rescued by overexpressing hyperactive ACA8 or ACA10. Furthermore, we show that BON1 has one high-affinity Ca2+ binding site in the VWA domain that is critical for activation of ACA8 as well as for BON1 function, suggesting a feedback mechanism for Ca2+ homeostasis at resting concentrations. Our findings suggest that this Ca2+ responsive regulatory mechanism extends beyond Arabidopsis, as we show interactions between ACA and BON proteins from algae to flowering plants, pointing to an ancient regulatory mechanism for maintaining low basal cytosolic Ca2+. Notably, a human plasma membrane-localized autoinhibited Ca2+ pump can also be activated by a human BON protein in a yeast functional assay system, suggesting evolutionary conservation in Ca2+ regulation across species.

Plant microRNAs enter the scene of calcium signaling

Recent studies have identified the miRNA391/1432/4376 superfamily (miR391S) in seed plants, which targets the 5' untranslated region (UTR) of mRNAs encoding autoinhibited Ca2+-ATPases (ACAs), a key component of calcium signaling. This superfamily includes miR391 in the Brassicaceae, miR4376 in the Solanaceae, and miR1432 in the Poaceae, all of which share a highly conserved 10-nucleotide (nt) core in their mature miRNA sequences. Notably, miR1432 in the Poaceae targets both ACA and mRNAs encoding calmodulin-like proteins, which are putative Ca2+ sensors. In this opinion article we highlight evidence revealing this miRNA superfamily's ancient origin, regulatory conservation, and sequence diversification linked to functional innovation. Consistent with the central role of calcium signaling, recent studies on Arabidopsis thaliana and rice suggest the broad implications of the ACA-targeting miRNAs in plant development, immunity, and abiotic stress responses.

CRISPR-Cas9 Mediated Gene Editing Platform Through Callus-to-Plant Regeneration and Functional Analysis of DoALA4─DoALA6 in Dendrobium officinale

Dendrobium orchids are well known for their great horticultural and medicinal values; however, the CRISPR/Cas9 gene editing system for Dendrobium species still needs to be improved. Therefore, this study aims to establish a CRISPR/Cas9-based functional validation system using Dendrobium officinale as a model species for the Dendrobium genus and to validate the DoALA4─DoALA6 genes, which may relate to growth and disease resistance. We first conducted a bioinformatics analysis of the P-type ATPase gene family in D. officinale, revealing the evolutionary diversity of P-type ATPase genes in orchids. Second, we inserted the GFP gene into the vector of CRISPR/Cas9 gene editing system to enhance the selection efficiency of genome-edited plants. Comparative analysis showed that different explants exhibited varying transformation efficiencies, ranging from 5% to 46.2%. Considering the regeneration capability, survival rate and gene editing efficiency, we selected callus as the transformation explant. Third, we used this editing system to generate DoALA4─DoALA6 mutants. Phenotypic observations of the mutants and inoculation of D. officinale with Sclerotium rolfsii indicated that DoALA4─DoALA6 are crucial for the growth of D. officinale and its resistance to southern blight disease. This efficient and stable CRISPR/Cas9 platform offers a foundation for further gene studies and Dendrobium breeding.

Phytochrome B regulates cortical microtubule arrangement to control cotyledon polar expansion by repressing LONGIFOLIAs

Light promotes the expansion and controls the directionality of expansion in cotyledons, transforming small oval cotyledons into larger orbicular shapes. However, the cellular basis underlying this polar expansion remains unclear. We report that cotyledon polar expansion in Arabidopsis (Arabidopsis thaliana) is primarily associated with the polar expansion of pavement cells, rather than with polar cell proliferation. Phytochrome B (phyB) promotes this polar expansion by inhibiting PHYTOCHROME INTERACTING FACTORs (PIFs), which normally suppress expansion and inversely regulate its directionality. PIFs exert their control over directionality partly through the activation of their target genes, LONGIFOLIAs (LNGs). At the cellular level, phyB decreases the number of transversely arranged cortical microtubules, while increasing the number of longitudinally arranged microtubules. This phyB-induced change in microtubule arrangement would strengthen transverse expansion while weakening longitudinal expansion. In contrast, PIFs regulate microtubule arrangements in the opposite manner. Downstream of the phyB-PIF pathway, LNGs preferentially increase transversely arranged cortical microtubules. Overall, our data support that the regulation of cortical microtubule orientation by the phyB-PIF-LNG pathway underlies how phyB weakens longitudinal expansion relative to transverse expansion while promoting pavement cell expansion to make orbicular cotyledons in the light.

Identification of candidate genes for drought tolerance in soybean through QTL mapping and gene expression analysis

Introduction

Drought stress significantly reduces soybean yield, underscoring the need to develop drought-resistant varieties and identify the underlying genetic mechanisms. However, the specific genes and pathways contributing to drought tolerance remain poorly understood. This study aimed to identify candidate genes associated with drought tolerance in soybean using a recombinant inbred line (RIL) population derived from PI416937 and Cheongsang.

Methods

A quantitative trait loci (QTL) mapping study using a 180K high-quality SNP array and composite interval mapping on 140 recombinant inbred lines, coupled with RNA sequencing of treated and control groups, was conducted to identify candidate genes for drought tolerance in soybean.

Results and Discussion

Through QTL mapping and differential gene expression profiling, five candidate genes were identified, with two (Glyma.06G076100 and Glyma.10G029600) highlighted as putative candidates based on functional annotations. These genes appear to play critical roles in stress tolerance, including ion homeostasis and the regulation of plasma membrane ATPase, as well as the synthesis of heat shock proteins (HSPs) that mitigate dehydration and thermal stress. These findings advance our understanding of the genetic basis of drought tolerance in soybean and provide valuable targets for breeding programs aimed at developing resilient cultivars.

Genome-wide identification of the P4ATPase gene family and its response to biotic and abiotic stress in soybean (Glycine max L.)

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. P4-ATPases (aminophospholipid ATPases, ALAs), one of the classes of P-type ATPases, can transport or flip phospholipids across membranes, creating and maintaining lipid asymmetry and playing crucial roles in plant growth and development. To date, however, the ALA gene family and its expression patterns under abiotic and biotic stresses have not been studied in the soybean genome.

RESULTS

A total of 27 GmALA genes were identified in the soybean genome and these genes were unevenly distributed on 15 chromosomes and classified into five groups based on phylogenetic analysis. The GmALAs family had diverse intron-exon patterns and a highly conserved motif distribution. A total of eight domains were found in GmALAs, and all GmALAs had conserved PhoLip_ATPase_C, phosphorylation and transmembrane domains. Cis-acting elements in the promoter demonstrated that GmALAs are associated with cellular development, phytohormones, environmental stress and photoresponsiveness. Analysis of gene duplication events revealed 24 orthologous gene pairs in soybean and synteny analysis revealed that GmALAs had greater collinearity with AtALAs than with OsALAs. Evolutionary constraint analyses suggested that GmALAs have undergone strong selective pressure for purification during the evolution of soybeans. Tissue-specific expression profiles revealed that GmALAs were differentially expressed in roots, stems, seeds, flowers, nodules and leaves. The expression pattern of these genes appeared to be diverse in the different developmental tissues. Combined transcriptome and qRT-PCR data confirmed the differential expression of GmALAs under abiotic (dehydration, saline, low temperature, ozone, light, wounding and phytohormones) and biotic stresses (aphid, fungi, rhizobia and rust pathogen).

CONCLUSION

In summary, genome-wide identification and evolutionary and expression analyses of the GmALAs gene family in soybean were conducted. Our work provides an important theoretical basis for further understanding GmALAs in biological functional studies.

Stress-responsive plasma membrane H+-ATPases regulate deep rooting in rice

Agricultural production is severely affected by environmental stresses such as drought, and deep rooting is an important factor enhancing crop drought avoidance. H+-ATPases provide a transmembrane proton gradient and are thought to play a crucial role in plant growth and abiotic stress responses. However, their expression under abiotic stress and function on deep rooting is poorly understood in rice. In this study, the conserved domains, potential phosphorylation sites, and three-dimensional structures of ten Oryza sativa PM H+-ATPases (OSAs) were analyzed. Quantitative PCR analysis revealed different expression patterns of these OSA genes under hormone treatment conditions (e.g., abscisic acid) and abiotic stress conditions (e.g., drought and salt stress). Subcellular localization analysis revealed that most OSA proteins were localized to the cell membrane. Phenotype determination of OSA mutants indicated that the ratio of deep rooting (RDR) of both osa7 and osa8 mutants was significantly reduced compared to that of wild-type rice plants. Additionally, OSA haplotypes in 268 rice accessions were analyzed, and the haplotypes associated with RDR were identified. The present results provide valuable information on crucial domains, expression patterns, and functional identification of OSA paralogs to reveal their role in rice responses to abiotic stress.

The P-type ATPase gene AHA5 is involved in proanthocyanidins accumulation in Medicago truncatula

Proanthocyanidins (PAs) are the second most abundant plant phenolic natural products. The proton membrane H+-ATPase (AHA) is required for PA transportation in vacuoles, but it remains unclear which AHA gene(s) encode tonoplast proton pump in M. truncatula. Here, we identified three Tnt1 mutant lines of MtAHA5, resulting in PAs deficit in seeds. MtAHA5 was preferentially expressed in developing seeds, exhibiting its highest transcript levels at early stages. Although MtAHA3, MtAHA4, and MtAHA9 shared similar transcript patterns with MtAHA5 and other structural genes involved in PA biosynthesis, their mutant lines did not exhibit any PA-deficit phenotypes. Subcellular localization analysis demonstrated that MtAHA5 is targeted to the tonoplast in tobacco leaves; conversely, MtAHA3 and MtAHA9 are localized to the cytoplasm, suggesting that MtAHA5 acts as a tonoplast proton pump but not MtAHA3 or MtAHA9. Further genetic analyses revealed that MtAHA5 could complement the PA-deficit phenotype in mtaha5 mutants and ataha10 mutants. Transient transcription assays indicated that MtAHA5 is activated by the MBW complex to regulate the PA accumulation. Collectively, our findings suggest that MtAHA5 serves as a tonoplast proton pump to generate the driving force for MATE1-mediated transport of PA precursors into vacuoles.

Plant Rho GTPase ROP6 Is Essential for Manganese Homeostasis in Arabidopsis

Manganese (Mn) is an indispensable mineral for plant growth and development. However, plants cultivated in acidic and poorly drained soils are vulnerable to Mn2+ toxicity due to its heightened increased bioavailability. Despite the crucial roles of the Rho of plant (ROP) GTPases in various cellular processes, their precise function in regulating Mn homeostasis remains elusive. In this study, we unveil a novel ROP6 GTPase signalling pathway that profoundly influences Mn phytotoxicity tolerance in Arabidopsis. Remarkably, the rop6 and dominant-negative ROP6 (rop6DN) mutant plants displayed a dramatically sensitive phenotype to Mn toxicity, whereas ROP6-overexpression and constitutively activated ROP6 (rop6CA) lines exhibited enhanced Mn stress tolerance. Immunoblot analysis corroborated that the ROP6 protein, especially the active form of ROP6, increased in abundance in the presence of high Mn levels. Further, we identified that ROP6 physically interacted and colocalized with Metal Tolerance Protein 8 (MTP8) in vivo. Mn transport complementation assays in yeast, combined with biochemical analyses, emphasized the essentiality of ROP6 for MTP8's transport activity. In addition, genetic analyses indicated that ROP6 acted upstream of MTP8 in the regulatory cascade. Collectively, our findings elucidate that ROP6 GTPase signalling positively modulates and enhances Mn stress tolerance in plants.

Identification and expression analysis of P-type ATPase IIIA subfamily in Puccinia Striiformis f. sp. tritici

BACKGROUND

Puccinia striiformis f. sp. tritici (Pst) causes wheat stripe (yellow) rust disease, which is one of the most destructive diseases affecting wheat worldwide. ATPases, a class of membrane proteins, play an important role in material exchange and signal transduction both within and outside biological cells by transporting ions and phospholipids. In plant pathogens, P-type ATPases primarily participate in pathogen development and virulence regulation. However, the P-type ATPase of subfamily IIIA (PMA) has not yet been identified in Pst. To investigate the potential functions of the PMA gene family in Pst, we conducted a genome-wide bioinformatics analysis and examined the expression profiles of the PMA gene family.

RESULTS

Six PMA genes were identified in the genome of P. striiformis f. sp. tritici (CYR34 race). The PMA proteins encoded by these genes ranged in length from 811 to 960 amino acids (aa). Each of the six PMA genes contained a typical ATPase IIIA H superfamily domain and was distributed across four chromosomes. Thirty-six major cis-regulatory elements were detected within the PMA gene family members. Elements such as the CGTCA-motif and TGACG-motif play significant roles in responding to environmental stresses and hormone signals. Quantitative PCR analysis revealed that the expression of the PMA04 gene was generally higher at 9 °C under various temperature stresses. The PMA06 gene typically exhibited higher expression levels at 16 °C. During the infection of Pst, the expression levels of PMA04, PMA05, and PMA06 were elevated at 72 h post treatment.

CONCLUSIONS

Our results indicate that the PMA gene family in the CYR34 strain comprises six PMA genes, which are crucial for managing temperature stress and pathogen infection, and exhibit a distinctive splicing pattern. This study not only identifies a target and direction for the development of new, efficient, and environmentally friendly control agents for wheat stripe rust but also establishes a foundation for analyzing its pathogenic mechanisms.

Advances of the mechanism for copper tolerance in plants

Copper (Cu) is a vital trace element necessary for plants growth and development. It acts as a co-factor for enzymes and plays a crucial role in various physiological processes, including photosynthesis, respiration, antioxidant systems, and hormone signaling transduction. However, excessive amounts of Cu can disrupt normal physiological metabolism, thus hindering plant growth, development, and reducing yield. In recent years, the widespread abuse of Cu-containing fungicides and industrial Cu pollution has resulted in significant soil contamination. Therefore, it is of utmost importance to uncover the adverse effects of excessive Cu on plant growth and delve into the molecular mechanisms employed by plants to counteract the stress caused by excessive Cu. Recent studies have confirmed the inhibitory effects of excess Cu on mineral nutrition, chlorophyll biosynthesis, and antioxidant enzyme activity. This review systematically outlines the ways in which plants tolerate excessive Cu stress and summarizes them into eight Cu-tolerance strategies. Furthermore, it highlights the necessity for further research to comprehend the molecular regulatory mechanisms underlying the responses to excessive Cu stress.

Transcriptome and metabolome analysis reveal the mechanisms of iron absorption differences in apple rootstocks under alkaline condition

Iron (Fe) is an essential micronutrient for plant growth and development. Fe deficiency leads to growth restriction, developmental disorders, chlorosis, and yield loss of fruit trees. This study investigated the molecular and biochemical mechanisms underlying the differences in Fe absorption among various apple rootstocks under alkaline conditions. Results showed that 'Oregon Spur II' grafted onto Qingzhen No.2 (OS/Q2) exhibited foliage etiolation, while 'Oregon Spur II' grafted onto Qingzhen No.1 (OS/Q1) did not display such etiolation under alkaline conditions. Physiological experiments revealed that total Fe, ferrous Fe, and chlorophyll content in OS/Q2 were significantly lower than those in OS/Q1, whereas the Fe reductase activity in OS/Q2 was higher than that in OS/Q1. Additionally, a total of 7,025 and 9,102 differentially expressed genes (DEGs), including 488 transcription factors (TFs), were identified in OS/Q1L vs. OS/Q2L and OS/Q1R vs. OS/Q2R, respectively. Subsequently, the pathways associated with "phenylpropanoid biosynthesis", "plant hormone signal transduction", "hydrogen ion export across plasma membrane", "heme binding", and "iron binding" were identified as critical for responding to Fe deficiency under alkaline conditions. Furthermore, a total of 244 differentially accumulated metabolites (DAMs) were identified in OS/Q1R vs. OS/Q2R. A combined analysis of the transcriptome and metabolome revealed that "ABC transporters", "biosynthesis of amino acids", and "carbon fixation in photosynthetic organisms" were significantly overrepresented in the KEGG pathways of both DEGs and DAMs. These newly acquired genes and metabolites involved in Fe metabolism will enhance our capacity to employ genetic engineering technologies to maintain Fe homeostasis in plants in the future.

Proteomic Insights into Trichome Responses to Elevated Elemental Stress in Cation Exchanger (CAX) Mutants

Research on elemental distribution in plants is crucial for understanding nutrient uptake, environmental adaptation and optimizing agricultural practices for sustainable food production. Plant trichomes, with their self-contained structures and easy accessibility, offer a robust model system for investigating elemental repartitioning. Transport proteins, such as the four functional cation exchangers (CAXs) in Arabidopsis, are low-affinity, high-capacity transporters primarily located on the vacuole. Mutants in these transporters have been partially characterized, one of the phenotypes of the CAX1 mutant being altered with tolerance to low-oxygen conditions. A simple visual screen demonstrated trichome density and morphology in cax1, and quadruple CAX (cax1-4: qKO) mutants remained unaltered. Here, we used synchrotron X-ray fluorescence (SXRF) to show that trichomes in CAX-deficient lines accumulated high levels of chlorine, potassium, calcium and manganese. Proteomic analysis on isolated Arabidopsis trichomes showed changes in protein abundance in response to changes in element accumulation. The CAX mutants showed an increased abundance of plasma membrane ATPase and vacuolar H-pumping proteins, and proteins associated with water movement and endocytosis, while also showing changes in proteins associated with the regulation of plasmodesmata. These findings advance our understanding of the integration of CAX transport with elemental homeostasis within trichomes and shed light on how plants modulate protein abundance under conditions of altered elemental levels.

Genome-Wide Identification and Expression Analysis of ACA/ECAs in Capsicum annuum L

Pepper (Capsicum annuum L.) is a popular vegetable in people's daily lives. During pepper growth, calcium (Ca) is an essential macronutrient, and calcium-transporting ATPase (ACA/ECA) is a vital protein for calcium transport. However, reports on the ACA/ECA gene family in the pepper genome are lacking. Hence, we used various bioinformatics methods to identify the ACA/ECA gene family in pepper. We identified eleven CaACA/ECA-family genes in pepper. The chromosomal distribution, phylogenetic evolution, characteristics, gene collinearity, gene and protein structures, cis-acting elements, and specific expression patterns of CaACA/ECAs were analyzed, revealing evolutionary relationships and correlations between CaACA/ECAs and other species (Arabidopsis, rice, and tomato). The experimental results indicate that CaACA/ECAs are stable and hydrophobic proteins, with each of the eleven CaACA/ECA proteins containing all ten motifs. Eleven CaACA/ECA genes are unevenly distributed on the eight chromosomes, and they substantially differ in the number of exons. We found a close correlation between the ACA/ECAs of pepper, Arabidopsis, and tomato. The CaACA/ECA genes contain various plant-hormone-, growth-, and stress-related cis-acting elements. The qRT-PCR results indicate that the expression levels of the eleven CaACA/ECAs exhibit differential temporal expression patterns under various exogenous Ca2+ concentrations. These results provide a theoretical basis for further studying the function of the pepper ACA/ECA gene family and valuable information for identifying and screening genes for pepper stress tolerance breeding.

Recent Advances in Understanding the Regulatory Mechanism of Plasma Membrane H+-ATPase through the Brassinosteroid Signaling Pathway

The polyhydroxylated steroid phytohormone brassinosteroid (BR) controls many aspects of plant growth, development and responses to environmental changes. Plasma membrane (PM) H+-ATPase, the well-known PM proton pump, is a central regulator in plant physiology, which mediates not only plant growth and development, but also adaptation to stresses. Recent studies highlight that PM H+-ATPase is at least partly regulated via the BR signaling. Firstly, the BR cell surface receptor BRASSINOSTEROID-INSENSITIVE 1 (BRI1) and multiple key components of BR signaling directly or indirectly influence PM H+-ATPase activity. Secondly, the SMALL AUXIN UP RNA (SAUR) gene family physically interacts with BRI1 to enhance organ development of Arabidopsis by activating PM H+-ATPase. Thirdly, RNA-sequencing (RNA-seq) assays showed that the expression of some SAUR genes is upregulated under the light or sucrose conditions, which is related to the phosphorylation state of the penultimate residue of PM H+-ATPase in a time-course manner. In this review, we describe the structural and functional features of PM H+-ATPase and summarize recent progress towards understanding the regulatory mechanism of PM H+-ATPase by BRs, and briefly introduce how PM H+-ATPase activity is modulated by its own biterminal regions and the post-translational modifications.

Conserved N-terminal Regulation of the ACA8 Calcium Pump with Two Calmodulin Binding Sites

The autoinhibited plasma membrane calcium ATPase ACA8 from A. thaliana has an N-terminal autoinhibitory domain. Binding of calcium-loaded calmodulin at two sites located at residues 42-62 and 74-96 relieves autoinhibition of ACA8 activity. Through activity studies and a yeast complementation assay we investigated wild-type (WT) and N-terminally truncated ACA8 constructs (Δ20, Δ30, Δ35, Δ37, Δ40, Δ74 and Δ100) to explore the role of conserved motifs in the N-terminal segment preceding the calmodulin binding sites. Furthermore, we purified WT, Δ20- and Δ100-ACA8, tested activity in vitro and performed structural studies of purified Δ20-ACA8 stabilized in a lipid nanodisc to explore the mechanism of autoinhibition. We show that an N-terminal segment between residues 20 and 35 including conserved Phe32, upstream of the calmodulin binding sites, is important for autoinhibition and the activation by calmodulin. Cryo-EM structure determination at 3.3 Å resolution of a beryllium fluoride inhibited E2 form, and at low resolution for an E1 state combined with AlphaFold prediction provide a model for autoinhibition, consistent with the mutational studies.

Understanding the role of P-type ATPases in regulating pollen fertility and development in pigeonpea

The P-type ATPase superfamily genes are the cation and phospholipid pumps that transport ions across the membranes by hydrolyzing ATP. They are involved in a diverse range of functions, including fundamental cellular events that occur during the growth of plants, especially in the reproductive organs. The present work has been undertaken to understand and characterize the P-type ATPases in the pigeonpea genome and their potential role in anther development and pollen fertility. A total of 59 P-type ATPases were predicted in the pigeonpea genome. The phylogenetic analysis classified the ATPases into five subfamilies: eleven P1B, eighteen P2A/B, fourteen P3A, fifteen P4, and one P5. Twenty-three pairs of P-type ATPases were tandemly duplicated, resulting in their expansion in the pigeonpea genome during evolution. The orthologs of the reported anther development-related genes were searched in the pigeonpea genome, and the expression profiling studies of specific genes via qRT-PCR in the pre- and post-meiotic anther stages of AKCMS11A (male sterile), AKCMS11B (maintainer) and AKPR303 (fertility restorer) lines of pigeonpea was done. Compared to the restorer and maintainer lines, the down-regulation of CcP-typeATPase22 in the post-meiotic anthers of the male sterile line might have played a role in pollen sterility. Furthermore, the strong expression of CcP-typeATPase2 in the post-meiotic anthers of restorer line and CcP-typeATPase46, CcP-typeATPase51, and CcP-typeATPase52 in the maintainer lines, respectively, compared to the male sterile line, clearly indicates their potential role in developing male reproductive organs in pigeonpea.

Identification of the potato (Solanum tuberosum L.) P-type ATPase gene family and investigating the role of PHA2 in response to Pep13

P-type ATPase family members play important roles in plant growth and development and are involved in plant resistance to various biotic and abiotic factors. Extensive studies have been conducted on the P-type ATPase gene families in Arabidopsis thaliana and rice but our understanding in potato remains relatively limited. Therefore, this study aimed to screen and analyze 48 P-type ATPase genes from the potato (Solanum tuberosum L.) genome database at the genome-wide level. Potato P-type ATPase genes were categorized into five subgroups based on the phylogenetic classification of the reported species. Additionally, several bioinformatic analyses, including gene structure analysis, chromosomal position analysis, and identification of conserved motifs and promoter cis-acting elements, were performed. Interestingly, the plasma membrane H+-ATPase (PM H+-ATPase) genes of one of the P3 subgroups showed differential expression in different tissues of potato. Specifically, PHA2, PHA3, and PHA7 were highly expressed in the roots, whereas PHA8 was expressed in potatoes only under stress. Furthermore, the small peptide Pep13 inhibited the expression of PHA1, PHA2, PHA3, and PHA7 in potato roots. Transgenic plants heterologously overexpressing PHA2 displayed a growth phenotype sensitive to Pep13 compared with wild-type plants. Further analysis revealed that reducing potato PM H+-ATPase enzyme activity enhanced resistance to Pep13, indicating the involvement of PM H+-ATPase in the physiological process of potato late blight and the enhancement of plant disease resistance. This study confirms the critical role of potato PHA2 in resistance to Pep13.

The asymmetric expression of plasma membrane H+-ATPase family genes in response to pulvinus-driven leaf phototropism movement in Vitis vinifera

Phototropism movement is crucial for plants to adapt to various environmental changes. Plant P-type H+-ATPase (HA) plays diverse roles in signal transduction during cell expansion, regulation of cellular osmotic potential and stomatal opening, and circadian movement. Despite numerous studies on the genome-wide analysis of Vitis vinifera, no research has been done on the P-type H+-ATPase family genes, especially concerning pulvinus-driven leaf movement. In this study, 55 VvHAs were identified and classified into nine distinct subgroups (1 to 9). Gene members within the same subgroups exhibit similar features in motif, intron/exon, and protein tertiary structures. Furthermore, four pairs of genes were derived by segmental duplication in grapes. Cis-acting element analysis identified numerous light/circadian-related elements in the promoters of VvHAs. qRT-PCR analysis showed that several genes of subgroup 7 were highly expressed in leaves and pulvinus during leaf movement, especially VvHA14, VvHA15, VvHA16, VvHA19, VvHA51, VvHA52, and VvHA54. Additionally, we also found that the VvHAs genes were asymmetrically expressed on both sides of the extensor and flexor cell of the motor organ, the pulvinus. The expression of VvHAs family genes in extensor cells was significantly higher than that in flexor cells. Overall, this study serves as a foundation for further investigations into the functions of VvHAs and contributes to the complex mechanisms underlying grapevine pulvinus growth and development.

The mechanism behind tenuazonic acid-mediated inhibition of plant plasma membrane H+-ATPase and plant growth

The increasing prevalence of herbicide-resistant weeds has led to a search for new herbicides that target plant growth processes differing from those targeted by current herbicides. In recent years, some studies have explored the use of natural compounds from microorganisms as potential new herbicides. We previously demonstrated that tenuazonic acid (TeA) from the phytopathogenic fungus Stemphylium loti inhibits the plant plasma membrane (PM) H+-ATPase, representing a new target for herbicides. In this study, we further investigated the mechanism by which TeA inhibits PM H+-ATPase and the effect of the toxin on plant growth using Arabidopsis thaliana. We also studied the biochemical effects of TeA on the PM H+-ATPases from spinach (Spinacia oleracea) and A. thaliana (AHA2) by examining PM H+-ATPase activity under different conditions and in different mutants. Treatment with 200 μM TeA-induced cell necrosis in larger plants and treatment with 10 μM TeA almost completely inhibited cell elongation and root growth in seedlings. We show that the isoleucine backbone of TeA is essential for inhibiting the ATPase activity of the PM H+-ATPase. Additionally, this inhibition depends on the C-terminal domain of AHA2, and TeA binding to PM H+-ATPase requires the Regulatory Region I of the C-terminal domain in AHA2. TeA likely has a higher binding affinity toward PM H+-ATPase than the phytotoxin fusicoccin. Finally, our findings show that TeA retains the H+-ATPase in an inhibited state, suggesting that it could act as a lead compound for creating new herbicides targeting the PM H+-ATPase.

Deficiencies in cluster-2 ALA lipid flippases result in salicylic acid-dependent growth reductions

P4 ATPases (i.e., lipid flippases) are eukaryotic enzymes that transport lipids across membrane bilayers. In plants, P4 ATPases are named Aminophospholipid ATPases (ALAs) and are organized into five phylogenetic clusters. Here we generated an Arabidopsis mutant lacking all five cluster-2 ALAs (ala8/9/10/11/12), which is the most highly expressed ALA subgroup in vegetative tissues. Plants harboring the quintuple knockout (KO) show rosettes that are 2.2-fold smaller and display chlorotic lesions. A similar but less severe phenotype was observed in an ala10/11 double KO. The growth and lesion phenotypes of ala8/9/10/11/12 mutants were reversed by expressing a NahG transgene, which encodes an enzyme that degrades salicylic acid (SA). A role for SA in promoting the lesion phenotype was further supported by quantitative PCR assays showing increased mRNA abundance for an SA-biosynthesis gene ISOCHORISMATE SYNTHASE 1 (ICS1) and two SA-responsive genes PATHOGENESIS-RELATED GENE 1 (PR1) and PR2. Lesion phenotypes were also reversed by growing plants in liquid media containing either low calcium (~0.1 mM) or high nitrogen concentrations (~24 mM), which are conditions known to suppress SA-dependent autoimmunity. Yeast-based fluorescent lipid uptake assays revealed that ALA10 and ALA11 display overlapping substrate specificities, including the transport of LysoPC signaling lipids. Together, these results establish that the biochemical functions of ALA8-12 are at least partially overlapping, and that deficiencies in cluster-2 ALAs result in an SA-dependent autoimmunity phenotype that has not been observed for flippase mutants with deficiencies in other ALA clusters.

OsACA9, an Autoinhibited Ca2+-ATPase, Synergically Regulates Disease Resistance and Leaf Senescence in Rice

Calcium (Ca2+) is a versatile intracellular second messenger that regulates several signaling pathways involved in growth, development, stress tolerance, and immune response in plants. Autoinhibited Ca2+-ATPases (ACAs) play an important role in the regulation of cellular Ca2+ homeostasis. Here, we systematically analyzed the putative OsACA family members in rice, and according to the phylogenetic tree of OsACAs, OsACA9 was clustered into a separated branch in which its homologous gene in Arabidopsis thaliana was reported to be involved in defense response. When the OsACA9 gene was knocked out by CRISPR/Cas9, significant accumulation of reactive oxygen species (ROS) was detected in the mutant lines. Meanwhile, the OsACA9 knock out lines showed enhanced disease resistance to both rice bacterial blight (BB) and bacterial leaf streak (BLS). In addition, compared to the wild-type (WT), the mutant lines displayed an early leaf senescence phenotype, and the agronomy traits of their plant height, panicle length, and grain yield were significantly decreased. Transcriptome analysis by RNA-Seq showed that the differentially expressed genes (DEGs) between WT and the Osaca9 mutant were mainly enriched in basal immune pathways and antibacterial metabolite synthesis pathways. Among them, multiple genes related to rice disease resistance, receptor-like cytoplasmic kinases (RLCKs) and cell wall-associated kinases (WAKs) genes were upregulated. Our results suggest that the Ca2+-ATPase OsACA9 may trigger oxidative burst in response to various pathogens and synergically regulate disease resistance and leaf senescence in rice.

A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.

Genome-Wide Identification and Expression Profiling of Heavy Metal ATPase (HMA) Genes in Peanut: Potential Roles in Heavy Metal Transport

The heavy metal ATPase (HMA) family belongs to the P-type ATPase superfamily and plays an essential role in the regulation of metal homeostasis in plants. However, the gene family has not been fully investigated in peanut. Here, a genome-wide identification and bioinformatics analysis was performed on AhHMA genes in peanut, and the expression of 12 AhHMA genes in response to Cu, Zn, and Cd was evaluated in two peanut cultivars (Silihong and Fenghua 1) differing in Cd accumulation. A total of 21 AhHMA genes were identified in the peanut genome, including ten paralogous gene pairs derived from whole-genome duplication, and an additional gene resulting from tandem duplication. AhHMA proteins could be divided into six groups (I-VI), belonging to two clades (Zn/Co/Cd/Pb-ATPases and Cu/Ag-ATPases). Most AhHMA proteins within the same clade or group generally have a similar structure. However, significant divergence exists in the exon/intron organization even between duplicated gene pairs. RNA-seq data showed that most AhHMA genes are preferentially expressed in roots, shoots, and reproductive tissues. qRT-PCR results revealed that AhHMA1.1/1.2, AhHMA3.1/3.2, AhHMA7.1/7.4, and AhHMA8.1 might be involved in Zn transport in peanut plants, while AhHMA3.2 and AhHMA7.5 might be involved in Cd transport. Our findings provide clues to further characterize the functions of AhHMA genes in metal uptake and translocation in peanut plants.

Plasma membrane-localized H+-ATPase OsAHA3 functions in saline-alkaline stress tolerance in rice

KEY MESSAGE

A novel function of plasma membrane-localized H+-ATPase, OsAHA3, was identified in rice, which is involved in saline-alkaline tolerance and specifically responds to high pH during saline-alkaline stress. Saline-alkaline stress causes serious damage to crop production on irrigated land. Plants suffer more severe damage under saline-alkaline stress than under salinity stress alone. Plasma membrane-localized proton (H+) pump (H+-ATPase) is an important enzyme that controls plant growth and development by catalyzing H+ efflux and enabling effective charge balance. Many studies about the role of plasma membrane H+-ATPases in saline-alkaline stress tolerance have been reported in Arabidopsis, especially on the AtAHA2 (Arabidopsis thaliana H+-ATPase 2) gene; however, whether and how plasma membrane H+-ATPases play a role in saline-alkaline stress tolerance in rice remain unknown. Here, using the activation-tagged rice mutant pool, we found that the plasma membrane-localized H+-ATPase OsAHA3 (Oryza sativa autoinhibited H+-ATPase 3) is involved in saline-alkaline stress tolerance. Activation-tagged line 29 (AC29) was identified as a loss-of-function mutant of OsAHA3 and showed more severe growth retardation under saline-alkaline stress with high pH than under salinity stress. Moreover, osaha3 loss-of-function mutants generated by CRISPR/Cas9 system exhibited saline-alkaline stress sensitive phenotypes; staining of leaves with nitrotetrazolium blue chloride (NBT) and diaminobenzidine (DAB) revealed more reactive oxygen species (ROS) accumulation in osaha3 mutants. OsAHA3-overexpressing plants showed increased saline-alkaline stress tolerance than wild-type plants. Tissue-specific expression analysis revealed high expression level of OsAHA3 in leaf, sheath, glume, and panicle. Overall, our results revealed a novel function of plasma membrane-localized H+-ATPase, OsAHA3, which is involved in saline-alkaline stress tolerance and specifically responds to high pH.

Sensing and regulation of plant extracellular pH

In plants, pH determines nutrient acquisition and sensing, and triggers responses to osmotic stress, whereas pH homeostasis protects the cellular machinery. Extracellular pH (pHe) controls the chemistry and rheology of the cell wall to adjust its elasticity and regulate cell expansion in space and time. Plasma membrane (PM)-localized proton pumps, cell-wall components, and cell wall-remodeling enzymes jointly maintain pHe homeostasis. To adapt to their environment and modulate growth and development, plant cells must sense subtle changes in pHe caused by the environment or neighboring cells. Accumulating evidence indicates that PM-localized cell-surface peptide-receptor pairs sense pHe. We highlight recent advances in understanding how plants perceive and maintain pHe, and discuss future perspectives.

Plant Ca2+-ATPases: From biochemistry to signalling

Calcium (Ca2+)-ATPases are ATP-dependent enzymes that transport Ca2+ ions against their electrochemical gradient playing the fundamental biological function of keeping the free cytosolic Ca2+ concentration in the submicromolar range to prevent cytotoxic effects. In plants, type IIB autoinhibited Ca2+-ATPases (ACAs) are localised both at the plasma membrane and at the endomembranes including endoplasmic reticulum (ER) and tonoplast and their activity is primarily regulated by Ca2+-dependent mechanisms. Instead, type IIA ER-type Ca2+-ATPases (ECAs) are present mainly at the ER and Golgi Apparatus membranes and are active at resting Ca2+. Whereas research in plants has historically focused on the biochemical characterization of these pumps, more recently the attention has been also addressed on the physiological roles played by the different isoforms. This review aims to highlight the main biochemical properties of both type IIB and type IIA Ca2+ pumps and their involvement in the shaping of cellular Ca2+ dynamics induced by different stimuli.

ZmHMA3, a Member of the Heavy-Metal-Transporting ATPase Family, Regulates Cd and Zn Tolerance in Maize

The pollution of heavy metals is extremely serious in China, including zinc (Zn), copper (Cu), lead (Pb), and cadmium (Cd). Heavy-metal-transporting ATPase (HMA) belongs to a subfamily of the P-ATPase family, which absorbs and transports Zn, Cu, Pb, and Cd in plants. Here, we describe a ZmHMA-encoding HMA family protein that positively regulates Cd and Zn tolerance. The real-time fluorescence quantification (RT-PCR) results revealed that ZmHMA3 had a high expression in B73, and the expression of ZmHMA3 was sensitive to Cd in yeast cells, which was related to Cd accumulation in yeast. Additionally, the Arabidopsis thaliana homologous mutants of AtHMA2 showed Cd sensitivity compared with WT. The overexpressing ZmHMA3 plants showed higher tolerance under Cd and Zn stresses than the wild type. The overexpression of ZmHMA3 led to higher Cd and Zn accumulation in tissues based on the subcellular distribution analysis. We propose that ZmHMA3 improves maize tolerance to Cd and Zn stresses by absorbing and transporting Cd and Zn ions. This study elucidates the gene function of the ZmHMA3 response to Cd and Zn stress and provides a reference for improving the characteristics of heavy metals enrichment in existing maize varieties and the plant remediation technology of heavy-metal-contaminated soil.

Zinc/iron-regulated transporter-like protein gene family in Theobroma cacao L: Characteristics, evolution, function and 3D structure analysis

The zinc/iron-regulated transporter-like protein (ZIP) gene family first identified in plants is highly distributed in the plant kingdom. This family has previously been reported to transport several essential and non-essential cationic elements, including those toxic to many economically important crops such as cacao (Theobroma cacao L.). In this article, we present a detailed study on physicochemical properties, evolution, duplication, gene structure, promoter region and TcZIP family three-dimensional protein structure. A total of 11 TcZIP genes have been identified to encode proteins from 309 to 435 aa, with localization in the plasma membrane and chloroplast, containing 6-9 putative domains (TM). Interspecies phylogenetic analysis subdivided the ZIP proteins into four groups. Segmental duplication events significantly contributed to the expansion of TcZIP genes. These genes underwent high pressure of purifying selection. The three-dimensional structure of the proteins showed that α helix conformations are predominant with several pocket sites, containing the metal binding site, with the residues leucine (LEU), alanine (ALA), glycine (GLY), serine (SER), lysine (LYS) and histidine (HIS) the most predicted. Regarding the analysis of the protein-protein interaction and enrichment of the gene ontology, four biological processes were assigned, the most important being the cation transport. These new discoveries expand the knowledge about the function, evolution, protein structures and interaction of ZIP family proteins in cacao and contribute to develop cacao genotypes enriched with important mineral nutrients as well as genotypes that bioaccumulate or exclude toxic metals.

Structural and Functional Diversity of Two ATP-Driven Plant Proton Pumps

Two ATP-dependent proton pumps function in plant cells. Plasma membrane H⁺-ATPase (PM H⁺-ATPase) transfers protons from the cytoplasm to the apoplast, while vacuolar H⁺-ATPase (V-ATPase), located in tonoplasts and other endomembranes, is responsible for proton pumping into the organelle lumen. Both enzymes belong to two different families of proteins and, therefore, differ significantly in their structure and mechanism of action. The plasma membrane H⁺-ATPase is a member of the P-ATPases that undergo conformational changes, associated with two distinct E1 and E2 states, and autophosphorylation during the catalytic cycle. The vacuolar H⁺-ATPase represents rotary enzymes functioning as a molecular motor. The plant V-ATPase consists of thirteen different subunits organized into two subcomplexes, the peripheral V₁ and the membrane-embedded V₀, in which the stator and rotor parts have been distinguished. In contrast, the plant plasma membrane proton pump is a functional single polypeptide chain. However, when the enzyme is active, it transforms into a large twelve-protein complex of six H⁺-ATPase molecules and six 14-3-3 proteins. Despite these differences, both proton pumps can be regulated by the same mechanisms (such as reversible phosphorylation) and, in some processes, such as cytosolic pH regulation, may act in a coordinated way.

Ectopic Expression of PvHMA2.1 Enhances Cadmium Tolerance in Arabidopsis thaliana

Cadmium (Cd) in soil inhibits plant growth and development and even harms human health through food chain transmission. Switchgrass (Panicum virgatum L.), a perennial C4 biofuel crop, is considered an ideal plant for phytoremediation due to its high efficiency in removing Cd and other heavy metals from contaminated soil. The key to understanding the mechanisms of switchgrass Cd tolerance is to identify the genes involved in Cd transport. Heavy-metal ATPases (HMAs) play pivotal roles in heavy metal transport, including Cd, in Arabidopsis thaliana and Oryza sativa, but little is known about the functions of their orthologs in switchgrass. Therefore, we identified 22 HMAs in switchgrass, which were distributed on 12 chromosomes and divided into 4 groups using a phylogenetic analysis. Then, we focused on PvHMA2.1, which is one of the orthologs of the rice Cd transporter OsHMA2. We found that PvHMA2.1 was widely expressed in roots, internodes, leaves, spikelets, and inflorescences, and was significantly induced in the shoots of switchgrass under Cd treatment. Moreover, PvHMA2.1 was found to have seven transmembrane domains and localized at the cell plasma membrane, indicating that it is a potential transporter. The ectopic expression of PvHMA2.1 alleviated the reduction in primary root length and the loss of fresh weight of Arabidopsis seedlings under Cd treatment, suggesting that PvHMA2.1 enhanced Cd tolerance in Arabidopsis. The higher levels of relative water content and chlorophyll content of the transgenic lines under Cd treatment reflected that PvHMA2.1 maintained water retention capacity and alleviated photosynthesis inhibition under Cd stress in Arabidopsis. The roots of the PvHMA2.1 ectopically expressed lines accumulated less Cd compared to the WT, while no significant differences were found in the Cd contents of the shoots between the transgenic lines and the WT under Cd treatment, suggesting that PvHMA2.1 reduced Cd absorption from the environment through the roots in Arabidopsis. Taken together, our results showed that PvHMA2.1 enhanced Cd tolerance in Arabidopsis, providing a promising target that could be engineered in switchgrass to repair Cd-contaminated soil.

Plant Plasma Membrane Proton Pump: One Protein with Multiple Functions

In plants, the plasma membrane proton pump (PM H⁺-ATPase) regulates numerous transport-dependent processes such as growth, development, basic physiology, and adaptation to environmental conditions. This review explores the multifunctionality of this enzyme in plant cells. The abundance of several PM H⁺-ATPase isogenes and their pivotal role in energizing transport in plants have been connected to the phenomena of pleiotropy. The multifunctionality of PM H⁺-ATPase is a focal point of numerous studies unraveling the molecular mechanisms of plant adaptation to adverse environmental conditions. Furthermore, PM H⁺-ATPase is a key element in plant defense mechanisms against pathogen attack; however, it also functions as a target for pathogens that enable plant tissue invasion. Here, we provide an extensive review of the PM H⁺-ATPase as a multitasking protein in plants. We focus on the results of recent studies concerning PM H⁺-ATPase and its role in plant growth, physiology, and pathogenesis.

Multiomics reveals an essential role of long-distance translocation in regulating plant cadmium resistance and grain accumulation in allohexaploid wheat (Triticum aestivum)

Cadmium (Cd) is a highly toxic heavy metal that readily enters cereals, such as wheat, via the roots and is translocated to the shoots and grains, thereby posing high risks to human health. However, the vast and complex genome of allohexaploid wheat makes it challenging to understand Cd resistance and accumulation. In this study, a Cd-resistant cultivar of wheat, 'ZM1860', and a Cd-sensitive cultivar, 'ZM32', selected from a panel of 442 accessions, exhibited significantly different plant resistance and grain accumulation. We performed an integrated comparative analysis of the morpho-physiological traits, ionomic and phytohormone profiles, genomic variations, transcriptomic landscapes, and gene functionality in order to identify the mechanisms underlying these differences. Under Cd toxicity, 'ZM1860' outperformed 'ZM32', which showed more severe leaf chlorosis, poorer root architecture, higher accumulation of reactive oxygen species, and disordered phytohormone homeostasis. Ionomics showed that 'ZM32' had a higher root-to-shoot translocation coefficient of Cd and accumulated more Cd in the grains than 'ZM1860'. Whole-genome re-sequencing (WGS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport between the two genotypes. Combined ionomics, transcriptomics, and functional gene analysis identified the plasma membrane-localized heavy metal ATPase TaHMA2b-7A as a crucial Cd exporter regulating long-distance Cd translocation in wheat. WGS- and PCR-based analysis of sequence polymorphisms revealed a 25-bp InDel site in the promoter region of TaHMA2b-7A, and this was probably responsible for the differential expression. Our multiomics approach thus enabled the identification of a core transporter involved in long-distance Cd translocation in wheat, and it may provide an elite genetic resource for improving plant Cd resistance and reducing grain Cd accumulation in wheat and other cereal crops.

Screening of protonstatin-1 (PS-1) analogs for improved inhibitors of plant plasma membrane H+-ATPase activity

We previously identified protonstatin-1 (PS-1) as a selective inhibitor of plasma membrane H⁺-ATPase (PM H⁺-ATPase) activity and used it as a tool to validate the chemiosmotic model for polar auxin transport. Here, to obtain compounds with higher affinity than PS-1 for PM H⁺-ATPase, we synthesized 34 PS-1 analogs and examined their ability to inhibit PM H⁺-ATPase activity. The 34 analogs showed varying inhibitory effects on the activity of this enzyme. The strongest effect was observed for the small molecule PS-2, which was approximately five times stronger than PS-1. Compared to PS-1, PS-2 was also a stronger inhibitor of auxin uptake as well as acropetal and basipetal polar auxin transport in Arabidopsis thaliana seedlings. Because PS-2 is a more potent inhibitor of PM H⁺-ATPase than PS-1, we believe that this compound could be used as a tool to study the functions of this key plant enzyme.

Regulation of pollen tube growth by cellular pH and ions

Tip growth of the pollen tube is a model system for the study of cell polarity establishment in flowering plants. The tip growth of the pollen tube displays an oscillating pattern corresponding to cellular ion and pH dynamics. Therefore, cellular pH and ions play an important role in pollen growth and development. In this review, we summarized the current advances in understanding the function of cellular pH and ions in regulating pollen tube growth. We analyzed the physiological roles and underlying mechanisms of cellular pH and ions, including Ca²⁺, K⁺, and Cl^-, in regulating pollen tube growth. We further examined the function of Ca²⁺ in regulating cytoskeletons, small G proteins, and cell wall development in relation to pollen tube growth. We also examined the regulatory roles of cellular pH in pollen tube growth as well as pH regulation of ion flow, cell wall development, auxin signaling, and cytoskeleton function in pollen. In addition, we assessed the regulation of pollen tube growth by proton pumps and the maintenance of pH homeostasis in the trans-Golgi network by ion transporters. The interplay of ion homeostasis and pH dynamics was also assessed. We discussed the unanswered questions regarding pollen tube growth that need to be addressed in the future.

Calcium channels and transporters: Roles in response to biotic and abiotic stresses

Calcium (Ca2+) serves as a ubiquitous second messenger by mediating various signaling pathways and responding to numerous environmental conditions in eukaryotes. Therefore, plant cells have developed complex mechanisms of Ca2+ communication across the membrane, receiving the message from their surroundings and transducing the information into cells and organelles. A wide range of biotic and abiotic stresses cause the increase in [Ca2+]cyt as a result of the Ca2+ influx permitted by membrane-localized Ca2+ permeable cation channels such as CYCLIC NUCLEOTIDE-GATE CHANNELs (CNGCs), and voltage-dependent HYPERPOLARIZATION-ACTIVATED CALCIUM2+ PERMEABLE CHANNELs (HACCs), as well as GLUTAMATE RECEPTOR-LIKE RECEPTORs (GLRs) and TWO-PORE CHANNELs (TPCs). Recently, resistosomes formed by some NUCLEOTIDE-BINDING LEUCINE-RICH REPEAT RECEPTORs (NLRs) are also proposed as a new type of Ca2+ permeable cation channels. On the contrary, some Ca2+ transporting membrane proteins, mainly Ca2+-ATPase and Ca2+/H+ exchangers, are involved in Ca2+ efflux for removal of the excessive [Ca2+]cyt in order to maintain the Ca2+ homeostasis in cells. The Ca2+ efflux mechanisms mediate the wide ranges of cellular activities responding to external and internal stimuli. In this review, we will summarize and discuss the recent discoveries of various membrane proteins involved in Ca2+ influx and efflux which play an essential role in fine-tuning the processing of information for plant responses to abiotic and biotic stresses.

Receptor-like protein kinase BAK1 promotes K+ uptake by regulating H+-ATPase AHA2 under low potassium stress

Potassium (K+) is one of the essential macronutrients for plant growth and development. However, the available K+ concentration in soil is relatively low. Plant roots can perceive low K+ (LK) stress, then enhance high-affinity K+ uptake by activating H+-ATPases in root cells, but the mechanisms are still unclear. Here, we identified the receptor-like protein kinase Brassinosteroid Insensitive 1-Associated Receptor Kinase 1 (BAK1) that is involved in LK response by regulating the Arabidopsis (Arabidopsis thaliana) plasma membrane H+-ATPase isoform 2 (AHA2). The bak1 mutant showed leaf chlorosis phenotype and reduced K+ content under LK conditions, which was due to the decline of K+ uptake capacity. BAK1 could directly interact with the AHA2 C terminus and phosphorylate T858 and T881, by which the H+ pump activity of AHA2 was enhanced. The bak1 aha2 double mutant also displayed a leaf chlorosis phenotype that was similar to their single mutants. The constitutively activated form AHA2Δ98 and phosphorylation-mimic form AHA2T858D or AHA2T881D could complement the LK sensitive phenotypes of both aha2 and bak1 mutants. Together, our data demonstrate that BAK1 phosphorylates AHA2 and enhances its activity, which subsequently promotes K+ uptake under LK conditions.

Physiological and Transcriptomic Responses of Illicium difengpi to Drought Stress

Illicium difengpi Kib and Kim, an endangered plant unique to karst areas in China, has evolved an extremely high tolerance to arid environments. To elucidate the molecular mechanisms of the response to drought stress in I. difengpi, physiological index determination and transcriptome sequencing experiments were conducted in biennial seedlings grown under different soil moisture conditions (70~80%, 40~50% and 10~20%). With increasing drought stress, the leaf chlorophyll content decreased, while the proline (Pro), soluble sugar (SS) and malondialdehyde (MDA) contents increased; superoxide dismutase (SOD) and peroxidase (POD) activities also increased. Transcriptome sequencing and pairwise comparisons of the treatments revealed 2489, 4451 and 753 differentially expressed genes (DEGs) in CK70~80 vs. XP40~50, CK70~80 vs. XP10~20 and XP40~50 vs. XP10~20, respectively. These DEGs were divided into seven clusters according to their expression trends, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment results of different clusters indicated that genes in the hormone signal transduction and osmotic regulation pathways were greatly activated under mild drought stress. When drought stress increased, the DEGs related to membrane system and protein modification and folding were all upregulated; simultaneously, chitin catabolism- and glycolysis/gluconeogenesis-related genes were continuously upregulated throughout drought stress, while the genes involved in photosynthesis were downregulated. Here, 244 transcription factors derived from 10 families were also identified. These results lay a foundation for further research on the adaptation of I. difengpi to arid environments in karst areas and the establishment of a core regulatory relationship in its drought resistance mechanism.

Testing the polar auxin transport model with a selective plasma membrane H+ -ATPase inhibitor

Auxin is unique among plant hormones in that its function requires polarized transport across plant cells. A chemiosmotic model was proposed to explain how polar auxin transport is derived by the H⁺ gradient across the plasma membrane (PM) established by PM H⁺ -adenosine triphosphatases (ATPases). However, a classical genetic approach by mutations in PM H⁺ -ATPase members did not result in the ablation of polar auxin distribution, possibly due to functional redundancy in this gene family. To confirm the crucial role of PM H⁺ -ATPases in the polar auxin transport model, we employed a chemical genetic approach. Through a chemical screen, we identified protonstatin-1 (PS-1), a selective small-molecule inhibitor of PM H⁺ -ATPase activity that inhibits auxin transport. Assays with transgenic plants and yeast strains showed that the activity of PM H⁺ -ATPases affects auxin uptake as well as acropetal and basipetal polar auxin transport. We propose that PS-1 can be used as a tool to interrogate the function of PM H⁺ -ATPases. Our results support the chemiosmotic model in which PM H⁺ -ATPase itself plays a fundamental role in polar auxin transport.

H+-ATPases in Plant Growth and Stress Responses

H⁺-ATPases, including the phosphorylated intermediate-type (P-type) and vacuolar-type (V-type) H⁺-ATPases, are important ATP-driven proton pumps that generate membrane potential and provide proton motive force for secondary active transport. P- and V-type H⁺-ATPases have distinct structures and subcellular localizations and play various roles in growth and stress responses. A P-type H⁺-ATPase is mainly regulated at the posttranslational level by phosphorylation and dephosphorylation of residues in its autoinhibitory C terminus. The expression and activity of both P- and V-type H⁺-ATPases are highly regulated by hormones and environmental cues. In this review, we summarize the recent advances in understanding of the evolution, regulation, and physiological roles of P- and V-type H⁺-ATPases, which coordinate and are involved in plant growth and stress adaptation. Understanding the different roles and the regulatory mechanisms of P- and V-type H⁺-ATPases provides a new perspective for improving plant growth and stress tolerance by modulating the activity of H⁺-ATPases, which will mitigate the increasing environmental stress conditions associated with ongoing global climate change.

The potential role of plasma membrane proteins in response to Zn stress in rice roots based on iTRAQ and PRM under low Cd condition

Cd pollution had already caused serious threats to crop growth and development, food safety and human health, and become a potential agricultural and global environmental problem. Zn had been used to reduce Cd accumulation in soil and plants. Proteins located in plasma membrane (PM) played important roles in transferring stress signals in plants. To further elucidate how PM proteins modulated Zn/Cd transport under low-Cd condition, quantitative proteomics was employed to identify and verify the differentially expressed proteins (DEPs) and their biological functions at proteome level. A total of 4008 proteins were identified, and 332 DEPs (192 up and 140 down, fold >1.50 or <0.66, p < 0.01) were screened. Functional analysis showed that DEPs were mainly catalytic active and binding proteins, involved in glutathione metabolism, phenylpropanoid biosynthesis, etc. DEPs involved in ion transport played key roles in regulating transmembrane transport, resisting stress and alleviating toxicity of heavy metals to rice roots. DEPs were as the marker proteins in rice root responding to heavy metal stress. This study had important guiding significances for metal ions transport mechanism and screening of biomarkers responding to abiotic stress, and provided references for further researches underlying abiotic stress and detoxication in rice and other plants.

Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.)

BACKGROUND

Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood.

RESULTS

Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61-26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain.

CONCLUSION

To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.

The molecular basis of zinc homeostasis in cereals

Plants require zinc (Zn) as an essential cofactor for diverse molecular, cellular and physiological functions. Zn is crucial for crop yield, but is one of the most limiting micronutrients in soils. Grasses like rice, wheat, maize and barley are crucial sources of food and nutrients for humans. Zn deficiency in these species therefore not only reduces annual yield but also directly results in Zn malnutrition of more than two billion people in the world. There has been good progress in understanding Zn homeostasis and Zn deficiency mechanisms in plants. However, our current knowledge of monocots, including grasses, remains insufficient. In this review, we provide a summary of our knowledge of molecular Zn homeostasis mechanisms in monocots, with a focus on important cereal crops. We additionally highlight divergences in Zn homeostasis of monocots and the dicot model Arabidopsis thaliana, as well as important gaps in our knowledge that need to be addressed in future research on Zn homeostasis in cereal monocots.

Mapping and functional analysis of high-copper accumulation mutant oshc1 in rice

Copper (Cu) is an essential but potentially toxic element in rice. Little is known about the mechanism of rice grain Cu accumulation. In this study, we identified a high copper accumulation in grain 1 (oshc1) mutant from the wild type indica rice cultivar 9311 (WT) mutant bank. Compared with those in WT, more Cu was shown to accumulate in the shoots of seedlings and the above-ground tissues except nodes although less total Cu content in oshc1. Further analysis showed that the mutant had an accelerated Cu transport ratio from roots to shoots and higher Cu concentration in xylem sap than WT. This phenomenon in oshc1 was controlled by a single recessive gene, which was identified as BGIOSGA007732, and named OsHMA4. The eight base frame-shift from 1021 to 1028 bp in the coding sequence of OsHMA4 led to a modification after the 341st amino acid and resulted in premature translation termination of OsHMA4 at the 377th amino acid. This may change the function of OsHMA4. Furthermore, the up-regulated OsCOPT7 and OsATX1 and down-regulated OsHMA4 probably decrease Cu compartmentalization in roots of oshc1. In summary, the frame-shift in OsHMA4 changes the function of OsHMA4 and the expression of genes relative to Cu transport in the mutant, which leads to more Cu transport upward and higher Cu accumulation in the rice grains. Moreover, oshc1 was more tolerance to Cu-shortage than WT, while more sensitive to Cu excess exposure than WT. However, RNA-Seq analysis shown that changes in transcription levels of genes in oshc1 involving in molecular function of ions binding and biological processes of cell wall organization and defense response to bio-stress. Which indicates that oshc1 is advantage to Cu limited condition than WT. This work reveals the mechanism of high Cu accumulation in the grains of oshc1 and provides a material to breed new cultivars with optimum levels of Cu in brown rice by crossing with other dominant varieties, which can be planted in different soils to ensure the yield and quality of rice.

Metal tolerance in plants: Molecular and physicochemical interface determines the "not so heavy effect" of heavy metals

An increase in technological interventions and ruthless urbanization in the name of development has deteriorated our environment over time and caused the buildup of heavy metals (HMs) in the soil and water resources. These heavy metals are gaining increased access into our food chain through the plant and/or animal-based products, to adversely impact human health. The issue of how to restrict the entry of HMs or modulate their response in event of their ingress into the plant system is worrisome. The current knowledge on the interactive-regulatory role and contribution of different physical, biophysical, biochemical, physiological, and molecular factors that determine the heavy metal availability-uptake-partitioning dynamics in the soil-plant-environment needs to be updated. The present review critically analyses the interactive overlaps between different adaptation and tolerance strategies that may be causally related to their cellular localization, conjugation and homeostasis, a relative affinity for the transporters, rhizosphere modifications, activation of efflux pumps and vacuolar sequestration that singly or collectively determine a plant's response to HM stress. Recently postulated role of gaseous pollutants such as SO₂ and other secondary metabolites in heavy metal tolerance, which may be regulated at the whole plant and/or tissue/cell is discussed to delineate and work towards a "not so heavy" response of plants to heavy metals present in the contaminated soils.

Promotion and Upregulation of a Plasma Membrane Proton-ATPase Strategy: Principles and Applications

Plasma membrane proton-ATPase (PM H+-ATPase) is a primary H+ transporter that consumes ATP in vivo and is a limiting factor in the blue light-induced stomatal opening signaling pathway. It was recently reported that manipulation of PM H+-ATPase in stomatal guard cells and other tissues greatly improved leaf photosynthesis and plant growth. In this report, we review and discuss the function of PM H+-ATPase in the context of the promotion and upregulation H+-ATPase strategy, including associated principles pertaining to enhanced stomatal opening, environmental plasticity, and potential applications in crops and nanotechnology. We highlight the great potential of the promotion and upregulation H+-ATPase strategy, and explain why it may be applied in many crops in the future.

Proton and calcium pumping P-type ATPases and their regulation of plant responses to the environment

Plant plasma membrane H+-ATPases and Ca2+-ATPases maintain low cytoplasmic concentrations of H+ and Ca2+, respectively, and are essential for plant growth and development. These low concentrations allow plasma membrane H+-ATPases to function as electrogenic voltage stats, and Ca2+-ATPases as "off" mechanisms in Ca2+-based signal transduction. Although these pumps are autoregulated by cytoplasmic concentrations of H+ and Ca2+, respectively, they are also subject to exquisite regulation in response to biotic and abiotic events in the environment. A common paradigm for both types of pumps is the presence of terminal regulatory (R) domains that function as autoinhibitors that can be neutralized by multiple means, including phosphorylation. A picture is emerging in which some of the phosphosites in these R domains appear to be highly, nearly constantly phosphorylated, whereas others seem to be subject to dynamic phosphorylation. Thus, some sites might function as major switches, whereas others might simply reduce activity. Here, we provide an overview of the relevant transport systems and discuss recent advances that address their relation to external stimuli and physiological adaptations.

Regulation of Cytosolic pH: The Contributions of Plant Plasma Membrane H+-ATPases and Multiple Transporters

Cytosolic pH homeostasis is a precondition for the normal growth and stress responses in plants, and H+ flux across the plasma membrane is essential for cytoplasmic pH control. Hence, this review focuses on seven types of proteins that possess direct H+ transport activity, namely, H+-ATPase, NHX, CHX, AMT, NRT, PHT, and KT/HAK/KUP, to summarize their plasma-membrane-located family members, the effect of corresponding gene knockout and/or overexpression on cytosolic pH, the H+ transport pathway, and their functional regulation by the extracellular/cytosolic pH. In general, H+-ATPases mediate H+ extrusion, whereas most members of other six proteins mediate H+ influx, thus contributing to cytosolic pH homeostasis by directly modulating H+ flux across the plasma membrane. The fact that some AMTs/NRTs mediate H+-coupled substrate influx, whereas other intra-family members facilitate H+-uncoupled substrate transport, demonstrates that not all plasma membrane transporters possess H+-coupled substrate transport mechanisms, and using the transport mechanism of a protein to represent the case of the entire family is not suitable. The transport activity of these proteins is regulated by extracellular and/or cytosolic pH, with different structural bases for H+ transfer among these seven types of proteins. Notably, intra-family members possess distinct pH regulatory characterization and underlying residues for H+ transfer. This review is anticipated to facilitate the understanding of the molecular basis for cytosolic pH homeostasis. Despite this progress, the strategy of their cooperation for cytosolic pH homeostasis needs further investigation.

Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with ⁶⁷ Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.

Natural variations in the P-type ATPase heavy metal transporter gene ZmHMA3 control cadmium accumulation in maize grains

Cadmium (Cd) accumulation in maize grains is detrimental to human health. Developing maize varieties with low Cd content is important for safe consumption of maize grains. However, the key genes controlling maize grain Cd accumulation have not been cloned. Here, we identified one major locus for maize grain Cd accumulation (qCd1) using a genome-wide association study (GWAS) and bulked segregant RNA-seq analysis with a biparental segregating population of Jing724 (low-Cd line) and Mo17 (high-Cd line). The candidate gene ZmHMA3 was identified by fine mapping and encodes a tonoplast-localized heavy metal P-type ATPase transporter. An ethyl methane sulfonate mutant analysis and an allelism test confirmed that ZmHMA3 influences maize grain Cd accumulation. A transposon in intron 1 of ZmHMA3 is responsible for the abnormal amino acid sequence in Mo17. Based on the natural sequence variations in the ZmHMA3 gene of diverse maize lines, four PCR-based molecular markers were developed, and these were successfully used to distinguish five haplotypes with different grain Cd contents in the GWAS panel and to predict grain Cd contents of widely used maize inbred lines and hybrids. These molecular markers can be used to breed elite maize varieties with low grain Cd contents.