A rice tonoplastic calcium exchanger, OsCCX2 mediates Ca2+/cation transport in yeast

Integrative analysis of the ABC gene family in sorghum revealed SbABCB11 participating in translocation of cadmium from roots to shoots

MAIN CONCLUSION

This study identified a SbABCB11 gene in sorghum that could enhance Cd translocation from roots to shoots, thus increasing Cd accumulation in shoots. Cadmium (Cd) is a widespread soil contaminant threatening human health. As an energy plant, sorghum (Sorghum bicolor (L.) Moench) has great potential in phytoremediation of Cd-polluted soils. ATP-binding cassette (ABC) transporters perform critical roles in transport of Cd. However, there has not yet been a comprehensive analysis of the ABC gene family in sorghum. In this study, 142 ABC genes in sorghum were identified. Transcriptome study showed 41 SbABCs with differential expression patterns under Cd treatment. Candidate gene-based association study for Cd translocation factors identified five significant SNPs inside the annotated gene SbABCB11. Sequence analysis in different haplotypes demonstrated there were multiple long indel variations in the coding region of SbABCB11. Expression study indicated that SbABCB11-Hap3 was upregulated in roots after Cd treatment. Yeast complementary assay proved that SbABCB11 participated in the efflux of Cd, which was further supported by the localization of SbABCB11 on the plasma membrane. Transient suppression of SbABCB11 via antisense oligodeoxyribonucleotide (asODN) method reduced Cd accumulation in the shoots of sorghum by decreasing the release of Cd into the xylem. Our results provide new insights into the potential roles of SbABCs in sorghum. We revealed that SbABCB11 participated in translocation of Cd from roots to shoots, and there were significant variations in the translocation ability among different haplotypes of SbABCB11. These findings will be of help for the molecular breeding of sorghum germplasms suitable for the phytoremediation of Cd-contaminated soils.

Jasmonic acid improves cadmium tolerance in rice (Oryza sativa) by reducing the production of nitric oxide

The involvement of jasmonic acid (JA) in the rice's response to cadmium (Cd) stress is well recognized, though the underlying mechanisms remain unclear. In this study, exposure to Cd stress rapidly elevated endogenous JA concentrations in rice roots, meanwhile, a mutant coleoptile photomorphogenesis 2 (cpm2) which produces less JA, was more sensitive to Cd stress than its wild type (WT). JA mitigated Cd toxicity by decreasing Cd absorption in root cell wall and shoot, which was achieved by up-regulating the expression of the Cd-chelation and efflux-related genes such as OsHMA3, OsABCG36 and OsCAL1; down-regulating the transcript level of the Cd uptake and translocation-related genes, including OsHMA2, OsCCX2, OsNRAMP1/5, and OsZIP5/7. Additionally, a reduction in hemicellulose content was observed in the root cell wall. Further analysis indicated that the mitigation effect of JA on Cd accumulation was dependent on the inhibition of nitric oxide (NO) synthesis, as the NO donor SNP could diminish this effect. In summary, JA effectively reduced Cd content in rice by modulating the cell wall's capacity for Cd uptake, potentially through reducing the production of NO.

MID1-COMPLEMENTING ACTIVITY regulates cell proliferation and development via Ca2+ signaling in Marchantia polymorpha

MID1-COMPLEMENTING ACTIVITY (MCA) is a land plant-specific, plasma membrane protein, and Ca2+ signaling component that responds to exogenous mechanical stimuli, such as touch, gravity, and hypotonic-osmotic stress, in various plant species. MCA is essential for cell proliferation and differentiation during growth and development in rice (Oryza sativa) and maize (Zea mays). However, the mechanism by which MCA mediates cell proliferation and differentiation via Ca2+ signaling remains unknown. Here, we address this question using the liverwort Marchantia polymorpha. We show that the M. polymorpha MCA ortholog, MpMCA, is highly expressed in actively dividing regions, such as apical notches in the thalli and developing gametangiophores, and that MpMCA is a plasma membrane protein. In vivo, Ca2+ imaging using a Ca2+ sensor (yellow cameleon) revealed that MpMCA is required for maintaining proper [Ca2+]cyt levels in the apical notch region, egg cells, and antheridium cells. Mpmca mutant plants showed severe cell proliferation and differentiation defects in the thalli, gametangiophores, and gametangia, resulting in abnormal development and unsuccessful fertilization. Furthermore, expression of the Arabidopsis MCA1 gene complemented most of the defects in the growth and development of the Mpmca mutant plants. Our findings indicate that MpMCA is an evolutionarily conserved Ca2+-signaling component that regulates cell proliferation and development across the life cycle of land plants.

Arabidopsis calcium-dependent protein kinases 4/5/6/11 negatively regulate hydrotropism via phosphorylation of MIZU-KUSSEI1

Hydrotropism facilitates the orientation of plant roots toward regions of elevated water potential, enabling them to absorb adequate water. Although calcium signaling plays a crucial role in plant response to water tracking, the exact regulatory mechanisms remain a mystery. Here, we employed the Arabidopsis (Arabidopsis thaliana) hydrotropism-specific protein MIZU-KUSSEI1 (MIZ1) as bait and found that calcium-dependent protein kinases 4/5/6/11 (CPK4/5/6/11) interacted with MIZ1 in vitro and in vivo. The cpk4/5/6/11 mutant exhibited increased sensitivity to water potential and enhanced root tip curvature. Furthermore, CPK4/5/6/11 primarily phosphorylated MIZ1 at Ser14/36 residues. Additionally, CPK-mediated phosphorylation of MIZ1 relieved its inhibitory effect on the activity of the endoplasmic reticulum-localized Ca2+ pump ECA1, altering the balance between cytoplasmic Ca2+ inflow and outflow, thereby negatively regulating the hydrotropic growth of plants. Overall, our findings unveil the molecular mechanisms by which the CPK4/5/6/11-MIZ1 module functions in regulating plant hydrotropism responses and provide a theoretical foundation for enhancing plant water use efficiency and promoting sustainable agriculture.

From stress to resilience: Unraveling the molecular mechanisms of cadmium toxicity, detoxification and tolerance in plants

Soil contamination with cadmium (Cd) has become a global issue due to increasing human activities. Cd contamination poses threats to plant growth as well as jeopardizing food safety and human health through the accumulation of Cd in edible parts of plants. Unraveling the Cd toxicity mechanisms and responses of plants to Cd stress is critical for promoting plant growth and ensuring food safety in Cd-contaminated soils. Toxicological research on plant responses to heavy metal stress has extensively studied Cd, as it can disrupt multiple physiological processes. In addition to morpho-anatomical, hormonal, and biochemical responses, plants rapidly initiate transcriptional modifications to combat Cd stress-induced oxidative and genotoxic damage. Various families of transcription factors play crucial roles in triggering such responses. Moreover, epigenetic modifications have been identified as essential players in maintaining plant genome stability under genotoxic stress. Plants have developed several detoxification strategies to mitigate Cd-induced toxicity, such as cell-wall binding, complexation, vacuolar sequestration, efflux, and translocation. This review provides a comprehensive update on understanding of molecular mechanisms involved in Cd uptake, transportation, and detoxification, with a particular emphasis on the signaling pathways that involve transcriptional and epigenetic responses in plants. This review highlights the innovative strategies for enhancing Cd tolerance and explores their potential application in various crops. Furthermore, this review offers strategies for increasing Cd tolerance and limiting Cd bioavailability in edible parts of plants, thereby improving the safety of food crops.

Shared signals, different fates: Calcium and ROS in plant PRR and NLR immunity

Lacking an adaptive immune system, plants rely on innate immunity comprising two main layers: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI), both utilizing Ca2+ influx and reactive oxygen species (ROS) for signaling. PTI, mediated by pattern-recognition receptors (PRRs), responds to conserved pathogen- or damage-associated molecular patterns. Some pathogens evade PTI using effectors, triggering plants to activate ETI. At the heart of ETI are nucleotide-binding leucine-rich repeat receptors (NLRs), which detect specific pathogen effectors and initiate a robust immune response. NLRs, equipped with a nucleotide-binding domain and leucine-rich repeats, drive a potent immune reaction starting with pronounced, prolonged cytosolic Ca2+ influx, followed by increased ROS levels. This sequence of events triggers the hypersensitive response-a localized cell death designed to limit pathogen spread. This intricate use of Ca2+ and ROS highlights the crucial role of NLRs in supplementing the absence of an adaptive immune system in plant innate immunity.

Ectopic overexpression of Eleusine coracana CAX3 confers tolerance to metal and ion stress in yeast and Arabidopsis

Ionic and metal toxicity in plants is still a global problem for the environment, agricultural productivity and ultimately poses human health threats when these metal ions accumulate in edible organs of plants. Metal and ion transport from cytosol to the vacuole is considered an important component of metal and ion tolerance and a plant's potential utility in phytoremediation. Finger millet (Eleusine coracana) is an orphan crop but has prominent nutritional value in comparison to other cereals. Previous transcriptomic studies suggested that one of the calcium/proton exchanger (EcCAX3) is strongly upregulated during different developmental stages of spikes development in plant. This finding led us to speculate that high calcium accumulation in the grain might be because of CAX3 function. Moreover, phylogenetic analysis shows that EcCAX3 is more closely related to foxtail millet, sorghum and rice CAX3 protein. To decipher the functional role of EcCAX3, we have adopted complementation of yeast triple mutant K677 (Δpmc1Δvcx1Δcnb1), which has defective calcium transport machinery. Furthermore, metal tolerance assay shows that EcCAX3 expression conferred tolerance to different metal stresses in yeast. The gain-of-function study suggests that EcCAX3 overexpressing Arabidopsis plants shows better tolerance to higher concentration of different metal ions as compared to wild type Col-0 plants. EcCAX3-overexpression transgenic lines exhibits abundance of metal transporters and cation exchanger transporter transcripts under metal stress conditions. Furthermore, EcCAX3-overexpression lines have higher accumulation of macro- and micro-elements under different metal stress. Overall, this finding highlights the functional role of EcCAX3 in the regulation of metal and ion homeostasis and this could be potentially utilized to engineer metal fortification and generation of stress tolerant crops in near future.

Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora

Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.

Polylactic acid microplastics have stronger positive effects on the qualitative traits of rice (Oryza sativa L.) than polyethylene microplastics: Evidence from a simulated field experiment

Soil pollution by microplastics (MPs) from different types of agricultural films has received substantial attention due to its potential effects on crop quality. To date, the effects of different types of MPs on rice grain quality and their underlying molecular mechanisms have not been clarified. In this study, we examined the effects of polyethylene MPs (PE-MPs) and biodegradable polylactic acid MPs (PLA-MPs) on rice grain quality at the environmental level (0.5 %) and evaluated the molecular mechanism through transcriptome analysis. PE- and PLA-MPs increased the number of rice grains per plant by 19.83 % and 24.66 %, respectively, and decreased the rice empty-shell rate by 55.89 % and 26.53 %, respectively. However, PLA-MPs increased the 1000-seed weight by 11.37 %, whereas PE-MPs had no obvious impact in this respect. Furthermore, MP exposure, especially that of PE-MPs, affected the content of mineral elements, fatty acids, and amino acids of rice grains by disturbing the expression of genes related to these functions and metabolism. Our findings provide insights into the response of rice grains to the stress caused by different MPs.

Golgi apparatus-localized CATION CALCIUM EXCHANGER4 promotes osmotolerance of Arabidopsis

Calcium (Ca2+) is a major ion in living organisms, where it acts as a second messenger for various biological phenomena. The Golgi apparatus retains a higher Ca2+ concentration than the cytosol and returns cytosolic Ca2+ to basal levels after transient elevation in response to environmental stimuli such as osmotic stress. However, the Ca2+ transporters localized in the Golgi apparatus of plants have not been clarified. We previously found that a wild-type (WT) salt-tolerant Arabidopsis (Arabidopsis thaliana) accession, Bu-5, showed osmotic tolerance after salt acclimatization, whereas the Col-0 WT did not. Here, we isolated a Bu-5 background mutant gene, acquired osmotolerance-defective 6 (aod6), which reduces tolerance to osmotic, salt, and oxidative stresses, with a smaller plant size than the WT. The causal gene of the aod6 mutant encodes CATION CALCIUM EXCHANGER4 (CCX4). The aod6 mutant was more sensitive than the WT to both deficient and excessive Ca2+. In addition, aod6 accumulated higher Ca2+ than the WT in the shoots, suggesting that Ca2+ homeostasis is disturbed in aod6. CCX4 expression suppressed the Ca2+ hypersensitivity of the csg2 (calcium sensitive growth 2) yeast (Saccharomyces cerevisiae) mutant under excess CaCl2 conditions. We also found that aod6 enhanced MAP kinase 3/6 (MPK3/6)-mediated immune responses under osmotic stress. Subcellular localization analysis of mGFP-CCX4 showed GFP signals adjacent to the trans-Golgi apparatus network and co-localization with Golgi apparatus-localized markers, suggesting that CCX4 localizes in the Golgi apparatus. These results suggest that CCX4 is a Golgi apparatus-localized transporter involved in the Ca2+ response and plays important roles in osmotic tolerance, shoot Ca2+ content, and normal growth of Arabidopsis.

MdHB7-like positively modulates apple salt tolerance by promoting autophagic activity and Na+ efflux

Salt stress adversely affects the yield and quality of crops and limits their geographical distribution. Studying the functions and regulatory mechanisms of key genes in the salt stress response is important for breeding crops with enhanced stress resistance. Autophagy plays an important role in modulating the tolerance of plants to various types of abiotic stressors. However, the mechanisms underlying salt-induced autophagy are largely unknown. Cation/Ca2+ exchanger proteins enhance apple salt tolerance by inhibiting Na+ accumulation but the mechanism underlying the response to salt stress remains unclear. Here, we show that the autophagy-related gene MdATG18a modulated apple salt tolerance. Under salt stress, the autophagic activity, proline content, and antioxidant enzyme activities were higher and Na+ accumulation was lower in MdATG18a-overexpressing transgenic plants than in control plants. The use of an autophagy inhibitor during the salt treatment demonstrated that the regulatory function of MdATG18a depended on autophagy. The yeast-one-hybrid assay revealed that the homeodomain-leucine zipper (HD-Zip) transcription factor MdHB7-like directly bound to the MdATG18a promoter. Transcriptional regulation and genetic analyses showed that MdHB7-like enhanced salt-induced autophagic activity by promoting MdATG18a expression. The analysis of Na+ efflux rate in transgenic yeast indicated that MdCCX1 expression significantly promoted Na+ efflux. Promoter binding, transcriptional regulation, and genetic analyses showed that MdHB7-like promoted Na+ efflux and apple salt tolerance by directly promoting MdCCX1 expression, which was independent of the autophagy pathway. Overall, our findings provide insight into the mechanism underlying MdHB7-like-mediated salt tolerance in apple through the MdHB7-like-MdATG18a and MdHB7-like-MdCCX1 modules. These results will aid future studies on the mechanisms underlying stress-induced autophagy and the regulation of stress tolerance in plants.

Transcriptional Regulatory Network of Plant Cadmium Stress Response

Cadmium (Cd) is a non-essential heavy metal with high toxicity to plants. Plants have acquired specialized mechanisms to sense, transport, and detoxify Cd. Recent studies have identified many transporters involved in Cd uptake, transport, and detoxification. However, the complex transcriptional regulatory networks involved in Cd response remain to be elucidated. Here, we provide an overview of current knowledge regarding transcriptional regulatory networks and post-translational regulation of the transcription factors involved in Cd response. An increasing number of reports indicate that epigenetic regulation and long non-coding and small RNAs are important in Cd-induced transcriptional responses. Several kinases play important roles in Cd signaling that activate transcriptional cascades. We also discuss the perspectives to reduce grain Cd content and improve crop tolerance to Cd stress, which provides a theoretical reference for food safety and the future research of plant varieties with low Cd accumulation.

Genome-wide association study to identify genomic loci associated with early vigor in bread wheat under simulated water deficit complemented with quantitative trait loci meta-analysis

A genome-wide association study (GWAS) was used to identify associated loci with early vigor under simulated water deficit and grain yield under field drought in a diverse collection of Iranian bread wheat landraces. In addition, a meta-quantitative trait loci (MQTL) analysis was used to further expand our approach by retrieving already published quantitative trait loci (QTL) from recombinant inbred lines, double haploids, back-crosses, and F2 mapping populations. In the current study, around 16%, 14%, and 16% of SNPs were in significant linkage disequilibrium (LD) in the A, B, and D genomes, respectively, and varied between 5.44% (4A) and 21.85% (6A). Three main subgroups were identified among the landraces with different degrees of admixture, and population structure was further explored through principal component analysis. Our GWAS identified 54 marker-trait associations (MTAs) that were located across the wheat genome but with the highest number found in the B sub-genome. The gene ontology (GO) analysis of MTAs revealed that around 75% were located within or closed to protein-coding genes. In the MQTL analysis, 23 MQTLs, from a total of 215 QTLs, were identified and successfully projected onto the reference map. MQT-YLD4, MQT-YLD9, MQT-YLD13, MQT-YLD17, MQT-YLD18, MQT-YLD19, and MQTL-RL1 contributed to the highest number of projected QTLs and were therefore regarded as the most reliable and stable QTLs under water deficit conditions. These MQTLs greatly facilitate the identification of putative candidate genes underlying at each MQTL interval due to the reduced confidence of intervals associated with MQTLs. These findings provide important information on the genetic basis of early vigor traits and grain yield under water deficit conditions and set the foundation for future investigations into adaptation to water deficit in bread wheat.

Advances in molecular mechanisms underlying cadmium uptake and translocation in rice

The increasing cadmium (Cd) pollution in paddy fields has severely threatened China's ecological and food safety. Cultivation of low Cd accumulation varieties to reduce Cd content in rice or cultivation of Cd-tolerant varieties for phytoremediation are considered effective methods to control Cd pollution in paddy fields. However, the underlying molecular mechanism of Cd absorption and transport by rice plants needs to be deciphered to cultivate these varieties. Here, we summarized the molecular mechanisms underlying Cd absorption and transport in rice, as well as the variation of Cd accumulation among rice varieties, the QTLs related to Cd accumulation in rice, and discusses the direction of future research.

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.

The signatures of organellar calcium

Recent insights about the transport mechanisms involved in the in and out of calcium ions in plant organelles, and their role in the regulation of cytosolic calcium homeostasis in different signaling pathways.

Ca2+-CBL-CIPK: a modulator system for efficient nutrient acquisition

Calcium (Ca²⁺) is a universal second messenger essential for the growth and development of plants in normal and stress situations. In plants, the proteins, CBL (calcineurin B-like) and CIPK (CBL-interacting protein kinase), form one of the important Ca²⁺ decoding complexes to decipher Ca²⁺ signals elicited by environmental challenges. Multiple interactors distinguish CBL and CIPK protein family members to form a signaling network for regulated perception and transduction of environmental signals, e.g., signals generated under nutrient stress conditions. Conservation of equilibrium in response to varying soil nutrient status is an important aspect for plant vigor and yield. Signaling processes have been reported to observe nutrient fluctuations as a signal responsible for regulated nutrient transport adaptation. Recent studies have identified downstream targets of CBL-CIPK modules as ion channels or transporters and their association in signaling nutrient disposal including potassium, nitrate, ammonium, magnesium, zinc, boron, and iron. Ca²⁺-CBL-CIPK pathway modulates ion transporters/channels and hence maintains a homeostasis of several important plant nutrients in the cytosol and sub-cellular compartments. In this article, we summarize recent literature to discuss the role of the Ca²⁺-CBL-CIPK pathway in cellular osmoregulation and homeostasis on exposure to nutrient excess or deprived soils. This further establishes a link between taking up the nutrient in the roots and its distribution and homeostasis during the generation of signal for the development and survival of plants.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BACKGROUND

Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.

RESULTS

In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.

CONCLUSION

The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BACKGROUND

Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity.

RESULTS

In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs.

CONCLUSION

The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Identification and Expression Profiling Analysis of the Cation/Ca2+ Exchanger (CCX) Gene Family: Overexpression of SlCCX1-LIKE Regulates the Leaf Senescence in Tomato Flowering Phase

Cation gradients in plant cellular compartments are maintained by the synergistic actions of various ion exchangers, pumps, and channels. Cation/Ca2+ exchanger (CCX) is one of the clades of the Ca2+/cation antiporter super family. Here, five SlCCX genes were identified in tomato. Sequence analysis indicated that SlCCXs have the conserved motifs as the CCX domain. Analysis of the expression level of each member of tomato CCX gene family under cation (Mg2+, Mn2+, Na+, and Ca2+) treatment was determined by qRT-PCR. Tomato CCX demonstrated different degrees of responding to cation treatment. Changes in SlCCX1-LIKE expression was induced by Mg2+ and Mn2+ treatment. Analysis of the expression of SlCCX genes in different tissues demonstrated that constitutive high expression of a few genes, including SlCCX1-LIKE and SlCCX5, indicated their role in tomato organ growth and development. Overexpression of SlCCX1-LIKE dramatically induced leaf senescence. Transcriptome analysis showed that genes related to ROS and several IAA signaling pathways were significantly downregulated, whereas ETH and ABA signaling pathway-related genes were upregulated in overexpression of SlCCX1-LIKE (OE-SlCCX1-LIKE) plants, compared with the wild type (WT). Moreover, overexpression of SlCCX1-LIKE plants accumulated more ROS content but less Mg2+ content. Collectively, the findings of this study provide insights into the base mechanism through which CCXs regulate leaf senescence in tomato.

Engineering cellular metabolite transport for biosynthesis of computationally predicted tropane alkaloid derivatives in yeast

Microbial biosynthesis of plant natural products (PNPs) can facilitate access to valuable medicinal compounds and derivatives. Such efforts are challenged by metabolite transport limitations, which arise when complex plant pathways distributed across organelles and tissues are reconstructed in unicellular hosts without concomitant transport machinery. We recently reported an engineered yeast platform for production of the tropane alkaloid (TA) drugs hyoscyamine and scopolamine, in which product accumulation is limited by vacuolar transport. Here, we demonstrate that alleviation of transport limitations at multiple steps in an engineered pathway enables increased production of TAs and screening of useful derivatives. We first show that supervised classifier models trained on a tissue-delineated transcriptome from the TA-producing plant Atropa belladonna can predict TA transporters with greater efficacy than conventional regression- and clustering-based approaches. We demonstrate that two of the identified transporters, AbPUP1 and AbLP1, increase TA production in engineered yeast by facilitating vacuolar export and cellular reuptake of littorine and hyoscyamine. We incorporate four different plant transporters, cofactor regeneration mechanisms, and optimized growth conditions into our yeast platform to achieve improvements in de novo hyoscyamine and scopolamine production of over 100-fold (480 μg/L) and 7-fold (172 μg/L). Finally, we leverage computational tools for biosynthetic pathway prediction to produce two different classes of TA derivatives, nortropane alkaloids and tropane N-oxides, from simple precursors. Our work highlights the importance of cellular transport optimization in recapitulating complex PNP biosyntheses in microbial hosts and illustrates the utility of computational methods for gene discovery and expansion of heterologous biosynthetic diversity.

Phylogenetic and ion-response analyses reveal a relationship between gene expansion and functional divergence in the Ca2+/cation antiporter family in Angiosperms

Plant CaCA superfamily genes with higher tendency to retain after WGD are more gene expression and function differentiated in ion-response. Plants and animals face different environmental stresses but share conserved Ca²⁺ signaling pathways, such as Ca²⁺/Cation transport. The Ca²⁺/cation antiporters superfamily (CaCAs) is an ancient and widespread family of ion-coupled cation transporters found in all kingdoms of life. We analyzed the molecular evolution progress of the family through comparative genomics and phylogenetics of CaCAs genes from plants and animals, grouping these genes into several families and clades, and identified multiple gene duplication retention events, particularly in the CAX (H⁺/cation exchanger), CCX (cation/Ca²⁺ exchanger), and NCL (Na⁺/Ca²⁺ exchanger-like) families. The tendency of duplication retention differs between families and gene clades. The gene duplication events were probably the result of whole-genome duplication (WGD) in plants and might have led to functional divergence. Tissue and ion-response expression analyses revealed that CaCAs genes with more highly differentiated expression patterns are more likely to be retained as duplicates than those with more conserved expression profiles. Phenotype of Arabidopsis thaliana mutants showed that loss of genes with a greater tendency to be retained after duplication resulted in more severe growth deficiency. CaCAs genes in salt-tolerant species tended to inherit the expression characteristics of their most recent common ancestral genes, with conservative ion-response expression. This study indicates a possible evolutionary scheme for cation transport and illustrates distinct fates and a mechanism for the evolution of gene duplicates. The increased copy numbers of genes and divergences in expression might have contributed to the divergent functions of CaCAs protein, allowing plants to cope with environmental stresses and adapt to a larger number of ecological niches.

Cation/Ca2+ Exchanger 1 (MdCCX1), a Plasma Membrane-Localized Na+ Transporter, Enhances Plant Salt Tolerance by Inhibiting Excessive Accumulation of Na+ and Reactive Oxygen Species

High salinity causes severe damage to plant growth and significantly reduces crop yields. The CCX family proteins can facilitate the transport of multiple ions to prevent toxicity. CCX proteins play an important role in regulating plant salt tolerance, but no detailed studies on CCX proteins in apples have been reported. Here, the CCX family gene MdCCX1 was cloned from apple (Malus domestica). It is constitutively expressed in various apple tissues and is significantly induced by salt stress. As a plasma membrane-localized protein, MdCCX1-overexpression could complement the Na⁺-sensitive phenotype of yeast mutants and reduce the Na⁺ content in yeast cells under NaCl treatment, suggesting that MdCCX1 could be a plasma membrane-localized Na⁺ transporter. To identify the function of MdCCX1 in salt response, we transformed this gene into Arabidopsis, apple calli, and apple plants. Overexpression of MdCCX1 significantly improved the salt tolerance of these transgenic materials. The significantly reduced Na⁺ content under NaCl treatment indicated that MdCCX1 overexpression could enhance plant salt tolerance by inhibiting the excessive accumulation of Na⁺. Besides, MdCCX1 overexpression could also enhance plant salt tolerance by promoting ROS scavenging. These findings provide new insight and rich resources for future studies of CCX proteins in plant species.

Characterization and Expression Analysis of the Ca2+/Cation Antiporter Gene Family in Tomatoes

The Ca²⁺/cation antiporter (CaCA) superfamily plays an important role in the regulation of the essential element Ca²⁺ and cation concentrations. Characterization and expression analyses of CaCA superfamily genes were performed in the tomato (Solanum lycopersicum) as a representative of dicotyledonous plants and fruit crops. Sixteen CaCA candidate genes were found and identified as tomato CaCA, SlCaCA, by a domain search. In a phylogenetic analysis of the SlCaCA superfamily, the 16 genes were classified into SlCAX, SlNCL, SlCCX, and SlMHX families. Among them, Solyc12g011070, belonging to the SlCAX family, had four splice variants, three of which were predicted to be nonfunctional because of a lack of important motifs. EF-hand domains were only found in SlNCL, in addition to consensus Na_Ca_ex domains, and the region containing EF-hand domains was characteristically long in some members of SlNCL. Furthermore, four genes of the SlCCX family were found to be intronless. As for intracellular localization, one SlCCX member was predicted to be localized to the plasma membrane, while other SlCCXs, SlCAXs, and SlMHXs were predicted to be localized to the vacuolar membrane. The expression patterns of SlCaCAs in various organs, including during several developmental stages of fruit, were classified into four groups. Genes involved in each of the SlCAX, SlNCL, and SlCCX gene families were categorized into three or four groups according to expression patterns, suggesting role sharing within each family. The main member in each subfamily and the members with characteristic fruit expression patterns included genes whose expression was regulated by sugar or auxin and that were highly expressed in a line having metabolite-rich fruit.

Calcium transport across plant membranes: mechanisms and functions

Contents Summary 49 I. Introduction 49 II. Physiological and structural characteristics of plant Ca²⁺ -permeable ion channels 50 III. Ca²⁺ extrusion systems 61 IV. Concluding remarks 64 Acknowledgements 64 References 64 SUMMARY: Calcium is an essential structural, metabolic and signalling element. The physiological functions of Ca²⁺ are enabled by its orchestrated transport across cell membranes, mediated by Ca²⁺ -permeable ion channels, Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers. Bioinformatics analysis has not determined any Ca²⁺ -selective filters in plant ion channels, but electrophysiological tests do reveal Ca²⁺ conductances in plant membranes. The biophysical characteristics of plant Ca²⁺ conductances have been studied in detail and were recently complemented by molecular genetic approaches. Plant Ca²⁺ conductances are mediated by several families of ion channels, including cyclic nucleotide-gated channels (CNGCs), ionotropic glutamate receptors, two-pore channel 1 (TPC1), annexins and several types of mechanosensitive channels. Key Ca²⁺ -mediated reactions (e.g. sensing of temperature, gravity, touch and hormones, and cell elongation and guard cell closure) have now been associated with the activities of specific subunits from these families. Structural studies have demonstrated a unique selectivity filter in TPC1, which is passable for hydrated divalent cations. The hypothesis of a ROS-Ca²⁺ hub is discussed, linking Ca²⁺ transport to ROS generation. CNGC inactivation by cytosolic Ca²⁺ , leading to the termination of Ca²⁺ signals, is now mechanistically explained. The structure-function relationships of Ca²⁺ -ATPases and Ca²⁺ /H⁺ exchangers, and their regulation and physiological roles are analysed.

Pharmacological Strategies for Manipulating Plant Ca2+ Signalling

Calcium is one of the most pleiotropic second messengers in all living organisms. However, signalling specificity is encoded via spatio-temporally regulated signatures that act with surgical precision to elicit highly specific cellular responses. How this is brought about remains a big challenge in the plant field, in part due to a lack of specific tools to manipulate/interrogate the plant Ca2+ toolkit. In many cases, researchers resort to tools that were optimized in animal cells. However, the obviously large evolutionary distance between plants and animals implies that there is a good chance observed effects may not be specific to the intended plant target. Here, we provide an overview of pharmacological strategies that are commonly used to activate or inhibit plant Ca2+ signalling. We focus on highlighting modes of action where possible, and warn for potential pitfalls. Together, this review aims at guiding plant researchers through the Ca2+ pharmacology swamp.

A Node-Expressed Transporter OsCCX2 Is Involved in Grain Cadmium Accumulation of Rice

Excessive cadmium (Cd) accumulation in grains of rice (Oryza sativa L.) is a risk to food security. The transporters in the nodes of rice are involved in the distribution of mineral elements including toxic elements to different tissues such as grains. However, the mechanism of Cd accumulation in grains is largely unknown. Here, we report a node-expressed transporter gene, OsCCX2, a putative cation/calcium (Ca) exchanger, mediating Cd accumulation in the grains of rice. Knockout of OsCCX2 caused a remarkable reduction of Cd content in the grains. Further study showed that disruption of this gene led to a reduced root-to-shoot translocation ratio of Cd. Moreover, Cd distribution was also disturbed in different levels of internode and leaf. OsCCX2 is localized to plasma membrane, and OsCCX2 is mainly expressed in xylem region of vascular tissues at the nodes. OsCCX2 might function as an efflux transporter, responsible for Cd loading into xylem vessels. Therefore, our finding revealed a novel Cd transporter involved in grain Cd accumulation, possibly via a Ca transport pathway in the nodes of rice.

Endoplasmic reticulum-localized CCX2 is required for osmotolerance by regulating ER and cytosolic Ca2+ dynamics in Arabidopsis

Ca²⁺ signals in plant cells are important for adaptive responses to environmental stresses. Here, we report that the Arabidopsis CATION/Ca²⁺ EXCHANGER2 (CCX2), encoding a putative cation/Ca²⁺ exchanger that localizes to the endoplasmic reticulum (ER), is strongly induced by salt and osmotic stresses. Compared with the WT, AtCCX2 loss-of-function mutant was less tolerant to osmotic stress and displayed the most noteworthy phenotypes (less root/shoot growth) during salt stress. Conversely, AtCCX2 gain-of-function mutants were more tolerant to osmotic stress. In addition, AtCCX2 partially suppresses the Ca²⁺ sensitivity of K667 yeast triple mutant, characterized by Ca²⁺ uptake deficiency. Remarkably, Cameleon Ca²⁺ sensors revealed that the absence of AtCCX2 activity results in decreased cytosolic and increased ER Ca²⁺ concentrations in comparison with both WT and the gain-of-function mutants. This was observed in both salt and nonsalt osmotic stress conditions. It appears that AtCCX2 is directly involved in the control of Ca²⁺ fluxes between the ER and the cytosol, which plays a key role in the ability of plants to cope with osmotic stresses. To our knowledge, Atccx2 is unique as a plant mutant to show a measured alteration in ER Ca²⁺ concentrations. In this study, we identified the ER-localized AtCCX2 as a pivotal player in the regulation of ER Ca²⁺ dynamics that heavily influence plant growth upon salt and osmotic stress.

Mechanisms of cytosolic calcium elevation in plants: the role of ion channels, calcium extrusion systems and NADPH oxidase-mediated 'ROS-Ca2+ Hub'

Elevation in the cytosolic free calcium is crucial for plant growth, development and adaptation. Calcium influx into plant cells is mediated by Ca2+ depolarisation-activated, hyperpolarisation-activated and voltage-independent Ca2+-permeable channels (DACCs, HACCs and VICCs respectively). These channels are encoded by the following gene families: (1) cyclic nucleotide-gated channels (CNGCs), (2) ionotropic glutamate receptors (GLRs), (3) annexins, (4) 'mechanosensitive channels of small (MscS) conductance'-like channels (MSLs), (5) 'mid1-complementing activity' channels (MCAs), Piezo channels, and hyperosmolality-induced [Ca2+]cyt. channel 1 (OSCA1). Also, a 'tandem-pore channel1' (TPC1) catalyses Ca2+ efflux from the vacuole in response to the plasma membrane-mediated Ca2+ elevation. Recent experimental data demonstrated that Arabidopsis thaliana (L.) Heynh. CNGCs 2, 5-10, 14, 16 and 18, GLRs 1.2, 3.3, 3.4, 3.6 and 3.7, TPC1, ANNEXIN1, MSL9 and MSL10,MCA1 and MCA2, OSCA1, and some their homologues counterparts in other species, are responsible for Ca2+ currents and/or cytosolic Ca2+ elevation. Extrusion of Ca2+ from the cytosol is mediated by Ca2+-ATPases and Ca2+/H+ exchangers which were recently examined at the level of high resolution crystal structure. Calcium-activated NADPH oxidases and reactive oxygen species (ROS)-activated Ca2+ conductances form a self-amplifying 'ROS-Ca2+hub', enhancing and transducing Ca2+ and redox signals. The ROS-Ca2+ hub contributes to physiological reactions controlled by ROS and Ca2+, demonstrating synergism and unity of Ca2+ and ROS signalling mechanisms.

Metal transport protein 8 in Camellia sinensis confers superior manganese tolerance when expressed in yeast and Arabidopsis thaliana

Manganese (Mn) is an important micronutrient element required for plant growth and development, playing catalytic roles in enzymes, membranes and DNA replication. The tea plant (Camellia sinensis) is able to accumulate high concentration of Mn without showing signs of toxicity, but the molecular mechanisms underlying this remain largely unknown. In this study, the C. sinensis cultivar ‘LJCY’ had higher Mn tolerance than cultivar ‘YS’, because chlorophyll content reduction was lower under the high Mn treatment. Proteomic analysis of the leaves revealed that C. sinensis Metal Tolerance Protein 8 (CsMTP8) accumulated in response to Mn toxicity in cultivar ‘LJCY’. The gene encoding CsMTP8, designated as CsMTP8 was also isolated, and its expression enhanced Mn tolerance in Saccharomyces cerevisiae. Similarly, the overexpression of CsMTP8 in Arabidopsis thaliana increased plant tolerance and reduced Mn accumulation in plant tissues under excess Mn conditions. Subcellular localization analysis of green florescence fused protein indicated that CsMTP8 was localized to the plasma membranes. Taken together, the results suggest that CsMTP8 is a Mn-specific transporter, which is localized in the plasma membrane, and transports excess Mn out of plant cells. The results also suggest that it is needed for Mn tolerance in shoots.

Arabidopsis CBL interacting protein kinase 3 interacts with ABR1, an APETALA2 domain transcription factor, to regulate ABA responses

Calcium (Ca²⁺) plays a vital role as a second messenger in several signaling pathways in plants. The calcineurin B-like proteins (CBLs) represent a family of plant calcium-binding proteins that function in propagating Ca²⁺ signals by interacting with CBL interacting protein kinases (CIPKs). Phosphorylation of CBL by CIPK is essential for the module to display full activity towards its target protein. Previous genetic analysis showed that the function of CBL9-CIPK3 module was implicated in negatively regulating seed germination and early development. In the present study, we have biochemically investigated the interaction of CBL9-CIPK3 module and our findings show that CBL9 is phosphorylated by CIPK3. Moreover, Abscisic acid repressor 1 (ABR1) is identified as the downstream target of CIPK3 and CIPK3-ABR1 function to regulate ABA responses during seed germination. Our study also indicates that the role of ABR1 is not limited to seed germination but it also regulates the ABA dependent processes in the adult stage of plant development. Combining our results, we conclude that the CBL9-CIPK3-ABR1 pathway functions to regulate seed germination and ABA dependent physiological processes in Arabidopsis.